I use a CF boot drive on my A4000T. It and an IDE DVD drive are on the motherboard IDE controller and my storage drive is on my WarpEngine.
I don't have any issues with booting off the CF card (4 GB), the OS (3.9 BB2) still loads quick enough.
IDE is fine for my Zip Drive. SCSI if you have it seems better for Amiga hard drives and CD/DVD drives.
