First, I know nothing of what was or was not in the Boss cars, never had that sort of money to own one, but I have to think logically. A 4 speed was a 4 speed and what did surprise me is the fact that Ford did NOT put the close ratio box in the Boss. That totally does not make sense to me at all. I mean they had a C/R box in the 429, why not in the Boss? ( it should have been standard in the Mach 1 as well!)
Anyway, maybe Steve can add light to this, but really, what engineering changes would there be between the earlier bellhousing and the later one. Afterall, the Cleveland was a brand new engine and considering Ford already had a usable bellhousing and a 4 speed, it was logical to use that bolt pattern. I suppose the depth of the housing might have changed, but I doubt the bolt pattern would.
Also is it not possible that at the casting foundry, they had the patterns for both the C5 housing and the later D1 and assuming there was no other changes, a foundry worker simply used the wrong set of patterns which might explain why later built car had older appearing bellhousings.
Sorry, but this is just how my "Spock" brain works.
As for my own Feb 71 Mach 1 4 speed, I have no idea what the bellhousing number is, I never paid attention to that when the motor was out a couple of times. Perhaps one day I'll look.