I agree that it is not important what the underlying hardware is, provided that it is adequate for the software, and that the desired software is supported on the combination of OS and architecture. Microsoft's Windows OS is currently available on a number of hardware platforms, including both x86 and Itanium.
The primary issue is not that the change is being made now, nor even that the target appears not to be optimal from a technology standpoint, but that it is being openly disclosed. The history of the computer industry is littered with the corpses of companies that said too much too soon and killed their existing portfolio. In that regard, I refuse to believe that Jobs is such an imbecile, and choose instead to posit that there are real strategic reasons for the timing of the announcement.
Apple have already stated that Intel chips will replace PowerPC chips. They have already stated that you won't be able to run MacOS on non-Apple grey box computers. They have already stated that they don't care if you run Windows on an Apple computer. The very speculation that the final target is x86 is just that, fueled by the knowledge that there is an existing MacOS port to that platform, and that developers now have access to an IA-32 x86 cross-compiler (along with big warnings stating that nothing is fixed in stone).
We've been through this on the Mac platform before, with the transition from 68K to PowerPC, and we had 'Fat binaries' for a time. Just as will be the case this time, that was a limited time offer, and its days have passed. Modern Apple software does not run on an MC68K Mac. Future Apple software will not run on a PowerPC Mac. It won't happen overnight - there's a few years left in the systems yet - but it will happen. The market desire for PowerPC Macs left millions of dollars of obsolete Apple inventory unsold in the channel. With the more streamlined 'just in time' manufacturing Apple currently uses, there will be much less inventory to write off, but sales will suffer, and they'll suffer badly.
Microsoft recently got into bed with IBM, selecting PowerPC as the platform for Xbox 360, and cutting Intel out of future platform sales. They also published a version of Windows XP that runs 64 bit clean on non-Itanium hardware, ensuring that the multi billion dollar Itanium platform is under further jeopardy. Although Itanium in its original form is very likely buried, even inside Intel, much of its technology will find its way into successors of EM64T. That there could be an alliance of Intel, Apple and HP pushing that technology as a MacOS platform should be viewed with some concern by both IBM and Microsoft.
Despite the very public announcement, clearly some cards are being carefully held close to the chest. Were that not the case it's unlikely that Jobs would have damaged the sales channel so badly and so early in a migration cycle.