I'm afraid that this has been asked more times before than I care to remember. There are some very good reasons why AOS should be ported to commodity PC hardware, but here are a few on the other side of the argument:
1) The A1 is definitely a lot less custom than previous Amiga hardware - it basically is "IBM PC style architecture", but with a PPC CPU.
2) If OS4 was on PC hardware, people would be able to use Windows applications, so there wouldn't be an incentive to develop OS4 applications.
3) The Amiga has been migrating to the PPC anyway - OS4 will be able to run WarpUP applications natively.
4) It would be impossible for Hyperion to support all possible x86 mobo configs - and if they only supported certain mobos/cards etc, people would buy it and complain it didn't work.
5) OS4 will have to go on embedded devices to pay it's way - PPC is a far more common platform for these than x86.
6) OS has to be released for Classic Amiga PPC at some point. Hyperion can only concentrate on one architecture at the moment, so PPC it is.
7) OS4 is now based on a fairly portable HAL (ExecSG is all C). If the custom hardware was to stop being avaliable, we wouldn't be too tied in as it could be ported across to another platform.