The only conditional checks in acfpgald before loading the bitstream are file related.
See
https://github.com/ps2dev/ps2sdk/blob/12994ed6649ebb1f2baa408843fb35df39896871/iop/arcade/acfpgald/src/fpgald.c
What I can tell by looking at acfpgald only is that there is no version or other sort of FPGA-targeted check before sending the bitstream to the FPGA using purely the address lines (data lines are fixed to zero).
The interface only supports PIO and MDMA/MWDMA. It does not support UDMA.
So a possible reason why it may not be compatible is the device doesn't support MWDMA, but I would need to probe at the device to figure out if that is the actual reason