OS X has a compatibility layer. This is what isolates the high level code of the programs from the hardware underneath. If a developer follows instructions (even Apple doesn't always do that!) then they only write to the OS. In the old days it was common to write directly to the hardware. When that changed, the software wouldn't work. That's what's behind the idea of software portability.
Mind you, it would still be a bear. I'm not for the idea. But it could be done.
That "compatibilty" is there, but you are obstucating the issue a bit by implying that the layer does some kind of conversion at runtime. Not so. People who write to the higher level ( all developers) will be abstracted from the hardware level, yes, but that does not imply some type of runtime emulation. On an intel machine the entire OS is compiled down to intel byte code, and the applications that run in that space are intel byte coded.
Big endianess is an issue only if the developer bypasses normal read/write API to write or read in data. I imagine that is negligible in the real world.
As for the non-technical issues. I see this as a total benefit.
1) The OS will not be licenced so no talk, please, about clones destroying OS X's marketshare. The nerds who install on Dell's this will be a tiny percentage.
2) OS X will have the top megahertz chips. Nobody cares about the technical ideologies behind the chips, but the speed.
3) Apple can port Cocoa to windows ( and thus the iLife suite) and allow dual booting of Mac based machines into windows. This will facilitate switching, and just people who want to buy an Apple branded machine. i know boatloads of people who would buy a mac if it could also run windows for a time. This is the only way that Apple could ever hope to get to 10% or more of the market again.
Then it is up to Apple to have a much better operating system than the Windows side , so that people who buy the mac for the Form Factor, for the brand etc. will switch to OS X rather than stay with Windows. For those of you who are Mac fans to deny this possibility, is a bit rich, no?
I think Apple is confident enough with OS X - and more importantly - with it's stellar trajectory to assume it can compete with windows on the same machine. they should however, start to reduce the cost of both the .Mac services and the annual(ish) update costs.