As far as I know, the only real difference is that the Yikes! logic board lacks an ADB port. I have the two sitting next to each other, so will double check on this.
Also, one of the firmware upgrades on the B&W motherboard "locked" their ability to recognize a G4 processor. Any ZIF upgrade you get for a B&W should include software to allow you to "unlock" it and work with a G4.
If you are using a B&W as your base, I'd suggest looking for a "Rev. B" Logic Board. These can accept two hard drives on the primary ATA bus, and have a few other upgrades. They also have a larger heatsink, although I would expect a 1ghz upgrade to include its own heatsink(the stock one gets a bit toasty even with a 450mhz G4 in my experience).