I can understand why Valley Forge is used westbound on the Schuylkill, since in practice the Valley Forge Interchange on the Turnpike is less a case of one road merging with another and more a case of the Schuylkill ending at the Turnpike, with each road having its own distinct identity separate from I-76. Plus, the King of Prussia interchange complex is where a significant amount of Schuylkill traffic (possibly more than half) splits off to US 202 (especially to the west), 422, and the rest of the connecting roads. I do think using Valley Forge itself is silly, though, and that King of Prussia would make far more sense, ideally with Harrisburg as a secondary control city wherever practical.
Eastbound on the Turnpike, though, I have no idea why Valley Forge is now used. It was originally only Philadelphia, with Valley Forge only turning up at PA 100 within the past decade and PA 29 since the move to AET. (From Morgantown west, it's still signed for Philadelphia.) I guess the idea might be that by this point, Philadelphia-bound traffic might be starting to fan out to get to various areas of the city, much like how New York City disappears as a control city from the northbound NJTP? This doesn't really make sense, though, as PA 100 and 29 only really serve the far Philadelphia suburbs, and don't even feed into the actual city in any way.
Interestingly, Valley Forge is never used at all on I-276 westbound; it's all just Harrisburg (and Allentown where "To I-476" is signed). This is even the case on the newest signs.
As for I-476, I imagine Plymouth Meeting is used for a similar reason to Valley Forge on the Schuylkill, especially since I-476 ended at the Turnpike until 1996. Now, though, while the Blue Route and Northeast Extension definitely have distinct identities like the Schuylkill and the Turnpike mainline, they do feed seamlessly into one another, making this less of a factor. A comparable situation would be if I-76 instead fed seamlessly onto the US 422 expressway. Signing Pottstown from Center City would make sense then, as signing Allentown from I-95 makes sense now. If a local control city must be used, though, I would prefer Conshohocken, with Allentown as a secondary control city wherever practical. North of the Schuylkill, Allentown could then be used exclusively.