Perhaps I've been lucky so far and I'm on the edge of that 4GB of data on my main boot partition or does the FASTATA4000 allow a bigger boot partition than standard IDE/SCSI controllers on an Amiga?
The 4GB limit is due to 32-bit addressing on:
-Commodore drivers (scsi.device)
-Commodore FFS
So if you have a 64-bit filesystem like PFS in the RDB and the drive is on a 64-bit controller (which I think the FastATA is), then you should be fine.
I think a custom kickstart ROM with scsi.device v43 and FFS v45 burned in would also be immune to 4GB issues, as would a system with those modules loaded into FlashROM (like Algor/Deneb). I do the latter, but I keep my boot partition within the 4GB limit in just in case I need to disable the Flash.