Yes, I'm quite aware of recent history. All you say is true (and I certainly know about the universal binaries; I just used the term I learned it under...that Xcode can do this is well-known).
However...I think that while Apple does a super job of making transitions easy, they care less about legacy than you suggest. This general direction is apparent in the direction they took with (yes, they backtracked, but I think this will be the exception) FCPX
I don't see another more away from a processor family, but the addition of one or two more, and we're not going to see a Rosetta-style program available for the new families to run Intel code; rather, anything new will just work, while older programs will run on Intel but not the new cpus. I doubt the App Store would carry anything that's not cross-compatible.
And not only that, this is in NeXTStep's DNA. That OS was made for portability, and ran on at least (if this link is accurate) four different processor families. Apple also had a concurrent build of OS X on Intel while they sold PowerPC machines. Fat Binaries also would allow Apple, if they felt like it, to make the CPU all but invisible to the user for properly recompiled programs, letting them have multiple processors in their lineup (this does, however, leave anything older or not recompiled out in the cold; that doesn't seem to matter much to Apple, however).
This is just smart business; something goes wrong with Intel, they're ready. A new, decent competitor pops up? port it, and if it proves to be better, run with it. To not to have these projects going would seem to be a mistake.