I agree that the IBX should definitely extend to this transfer station with PSA, but they (IBX and PSA) really should do more than that (in later phases). For PSA, clearly the Astoria station is very difficult, and the Sunnyside station is probably legitimately difficult due to the grade and underpass where it would be built. That one could be rebuilt, and eventually it probably should, but they're probably right that it'd be too expensive to do so today. But they should build a station at Northern Blvd where it intersects QBL, where an easy transfer can be made, and where's there's room to expand the embankment.
For the IBX, they should be able to extend it over Hell Gate to the Bronx, though it will be logistically difficult with freight. The two western tracks can serve Amtrak and Metro North as they plan to currently, and freight can run on those tracks at night (this is the difficult part; I could be done, but would need much more precise freight ops than there are currently). And IBX can use the two eastern tracks (the 4th track being rebuilt), with a fence in-between for FRA-compliance. Once in the Bronx, the IBX could extend along the NEC, which has room for 6 tracks all the way to Pelham Bay, or it could turn west somewhere. The crosstown route, perhaps tunneled to Yankee Stadium, or over a capped Cross Bronx Expressway to Fort Lee, would obviously be ideal for connectivity, but definitely more expensive. Paralleling PSA is not ideal, though, even the IBX could bring far higher headways and 24/7 service, and also have more stations. Hopefully once the IBX is open and sees success, a Bronx Hell Gate extension will be studied. The state budget came close to funding a study of this (it was in the Senate Budget, but did not make the finalized budget, just like QueensLink).
vanshookeraggen had some cogent comments on reddit/r/nycrail, which I believe you have seen.
I doubt that East Bronx - Queens rider volume will ever be great enough to justify extending the IBX to the Bronx. It will be hard enough to justify a PSA - IBX transfer in Queens.
Penn Station Access is a disaster waiting to happen. It will only cause more interlining with LIRR & AMTRAK. What you just stated about 102 Metro-North trains expected to serve Penn Station will greatly reduce capacity for service to Grand Central and the New Haven Line. Penn Station does not have the capacity for MNR or CT Rail because both LIRR/NJT occupy Penn Station and Penn Station makes up the bulk of both the LIRR/NJT's ridership. So if you want service from the MNR to Penn Station more railcars would have to be ordered LIRR and/or NJT have to go or reduced service on one/both which will cause a disaster for NY's economy. You are going to run up against capacity at Penn Station which will greatly reduce AMTRAK service as well due to the fact that AMTRAK does not run as frequently. I doubt that Penn Access will see many riders unless there is fare integration with the subway including subway preference towards Manhattan. The TriboroRX extension to the Bronx is feasible since Hunts Point is a transit desert with the extension avoiding interlining with AMTRAK. It's bad enough that the East & North River Tunnels are damaged, MNR will only worsen the problem that AMTRAK has.
vanshookeraggen we're talking about this some more elsewhere. It seems that a lot of these curves will be too sharp for platforms (~1000 m curves are needed) without curve straightening. At Northern Blvd, that would require some property takings, probably that Michaels/Subway building. At the IBX-PSA junction, there's enough straight platform, but it'd be better with straightened curves so the trains can be closer to the junction. Another possibility, though, is train-based gap fillers. Ones like these in Europe (https://www.reddit.com/r/transit/comments/vml9fm/z%C3%BCrich_sbahn_trains_have_level_boarding_from/) are quite good, and they would solve all of these issues. In fact, the FRA was close to mandating gap fillers altogether in 2020. Nevertheless, it is true that any northern IBX extension will undoubtedly be more expensive due to things like straightening curves for platforms, buying gap filler trains, tunneling under the BQE off ramp just north of Roosevelt, etc. As for ridership, IMO there's a lot of latent demand for Bronx-Queens travel, but we'll definitely have to see about that. Hopefully the IBX up to Jackson Heights proves successful enough that a northern extension is more viable.
I agree that the IBX should definitely extend to this transfer station with PSA, but they (IBX and PSA) really should do more than that (in later phases). For PSA, clearly the Astoria station is very difficult, and the Sunnyside station is probably legitimately difficult due to the grade and underpass where it would be built. That one could be rebuilt, and eventually it probably should, but they're probably right that it'd be too expensive to do so today. But they should build a station at Northern Blvd where it intersects QBL, where an easy transfer can be made, and where's there's room to expand the embankment.
For the IBX, they should be able to extend it over Hell Gate to the Bronx, though it will be logistically difficult with freight. The two western tracks can serve Amtrak and Metro North as they plan to currently, and freight can run on those tracks at night (this is the difficult part; I could be done, but would need much more precise freight ops than there are currently). And IBX can use the two eastern tracks (the 4th track being rebuilt), with a fence in-between for FRA-compliance. Once in the Bronx, the IBX could extend along the NEC, which has room for 6 tracks all the way to Pelham Bay, or it could turn west somewhere. The crosstown route, perhaps tunneled to Yankee Stadium, or over a capped Cross Bronx Expressway to Fort Lee, would obviously be ideal for connectivity, but definitely more expensive. Paralleling PSA is not ideal, though, even the IBX could bring far higher headways and 24/7 service, and also have more stations. Hopefully once the IBX is open and sees success, a Bronx Hell Gate extension will be studied. The state budget came close to funding a study of this (it was in the Senate Budget, but did not make the finalized budget, just like QueensLink).
vanshookeraggen had some cogent comments on reddit/r/nycrail, which I believe you have seen.
I doubt that East Bronx - Queens rider volume will ever be great enough to justify extending the IBX to the Bronx. It will be hard enough to justify a PSA - IBX transfer in Queens.
Penn Station Access is a disaster waiting to happen. It will only cause more interlining with LIRR & AMTRAK. What you just stated about 102 Metro-North trains expected to serve Penn Station will greatly reduce capacity for service to Grand Central and the New Haven Line. Penn Station does not have the capacity for MNR or CT Rail because both LIRR/NJT occupy Penn Station and Penn Station makes up the bulk of both the LIRR/NJT's ridership. So if you want service from the MNR to Penn Station more railcars would have to be ordered LIRR and/or NJT have to go or reduced service on one/both which will cause a disaster for NY's economy. You are going to run up against capacity at Penn Station which will greatly reduce AMTRAK service as well due to the fact that AMTRAK does not run as frequently. I doubt that Penn Access will see many riders unless there is fare integration with the subway including subway preference towards Manhattan. The TriboroRX extension to the Bronx is feasible since Hunts Point is a transit desert with the extension avoiding interlining with AMTRAK. It's bad enough that the East & North River Tunnels are damaged, MNR will only worsen the problem that AMTRAK has.
vanshookeraggen we're talking about this some more elsewhere. It seems that a lot of these curves will be too sharp for platforms (~1000 m curves are needed) without curve straightening. At Northern Blvd, that would require some property takings, probably that Michaels/Subway building. At the IBX-PSA junction, there's enough straight platform, but it'd be better with straightened curves so the trains can be closer to the junction. Another possibility, though, is train-based gap fillers. Ones like these in Europe (https://www.reddit.com/r/transit/comments/vml9fm/z%C3%BCrich_sbahn_trains_have_level_boarding_from/) are quite good, and they would solve all of these issues. In fact, the FRA was close to mandating gap fillers altogether in 2020. Nevertheless, it is true that any northern IBX extension will undoubtedly be more expensive due to things like straightening curves for platforms, buying gap filler trains, tunneling under the BQE off ramp just north of Roosevelt, etc. As for ridership, IMO there's a lot of latent demand for Bronx-Queens travel, but we'll definitely have to see about that. Hopefully the IBX up to Jackson Heights proves successful enough that a northern extension is more viable.