Perhaps, but this is what I've been hearing about Android from the moaners. Yes it will run, but the screen res might be different or the buttons may be different or perhaps the camera may or may not be there. Or even one may run faster than another due to different CPU/GPU those type of remarks.
All Which you could also apply to the Mac and OSX really, and of course Windows. No one has really been saying apps won't run, but rather there are options that the programmer may have to allow for.
Perhaps I'm being optimistic, but I think this will all sort itself out before very long and am accepted spec won't be that far off.
That's why Apple have made guidelines for developing programs (and user interfaces) for Mac OS X.
The fragmentation you are seeing on desktop computers are purely down to different OS versions (e.g. 10.4 Tiger, 10.5 Leopard and 10.6 Snow leopard).
This is for a lack of better words simply a non-issue.