I've done a little more research on this, and it's amazing how much of the northeast corridor FM dial was already locked in place by 1963-64, when 101.1 and 100.3 came on the scene in the Philly market.
They weren't necessarily at full class B facilities yet, but here's what was already on the scene, blocking any large-scale moves:
99.1 - New Haven, Binghamton, Zarephath, Annapolis
99.3 (class A channel)
99.5 - Lowell, Schenectady, NYC, Wilmington, Washington
99.7 -
99.9 - Bridgeport, Easton, Frederick MD (but no Ocean City yet)
100.1 (class A channel)
100.3 - Newark NJ, Media PA, Washington
100.5 - New Britain CT
100.7 - Boston, Allentown, Peekskill, Wildwood NJ
100.9 (class A channel)
101.1 - NYC, Philadelphia, Washington
101.3 - Scranton, Lancaster, Hamden CT
101.5 - Poughkeepsie, Trenton, Poughkeepsie, Waynesboro PA, Fredericksburg VA
101.7 (class A channel)
That would already have been a lot of signals to shuffle. Without looking at the spacing rules as they existed in 1963, it's hard for me to say if a full-scale realignment was possible. My guess is that even if it had been possible to somehow rearrange things to get Philadelphia to 100.5/101.3 instead of 100.3/101.1, it would have created some even uglier short-spacings along the way.
It's interesting to note, though, how relatively empty some of those channels were - there was nothing at all in the northeast on 99.7B back then, for instance, and those class A channels were nearly vacant as well. If the FCC had relaxed the distinction between class A and B channels, even if only in Zone I, things could have ended up very different back then.