I know that someone else has already built a desktop A1200 with a BPPC and BVision inside, he reprayed the case and everything - it looked absolutely fantastic, but he had to think about fitting feet to the bottom of the A1200 to physically raise the A1200 and give it ground clearence, primarily for air flow purposes. If I remember, this was the 68040 version of the BPPC which probably isn't recommended for desktop use!
I'd definately recommend a 68060 based BPPC for that sort of thing, but I don't feel that much improved cooling would be necessary, I think it'd definately be workable. Afterall, with OS4 running on there the 68060 itself would see very little use, and the PPC already has a nice heatsink with a small fan integrated into the unit. If you could improve on the PPC's cooling and provide some cooling for the BVision then I think that may pass ok.
I saw an A1200 desktop with a laptop's CDR drive mounted in it as well once... it'd be fantastic if that could be included as well!! But maybe that's taking things a little too far.
Brian