Yes and no.
They are identical for the A4000 and A3000 except that they physically removed the last two memory slots because putting memory in there would physically block the floppy drive. Other than that, there is no difference. I'm running a A4000 version in a A3000 right now and have been for quite a while(It's running my web server). I hope that helps!
Oh, btw, if you plan to do this, and plan to use the one board SCSI on the warp engine, you should check out the int 21(I think) hack. It's posted around somewhere. You may not need it if you are running a newer rev motherboard than I am(don't remember the rev). Otherwise the SCSI is VERY slow.