Correct, the 64MB of mainboard memory assignment can be changed by OSD config. This modifies settings in the FPGA hardware. Changes are updated on reset.
The Amiga core already contains enhanced RTG graphics and 16 bit audio (DAC is 24 bit). ChaosLord is correct in that even a legacy graphics card will offer better 2D performance, but this is something we can maybe address in the FPGA. The DDR2 memory for bursts should outperform old VRAM.
In theory you could have a daughterboard which has a number of PCI sockets directly connected to the main board, although I need to check the IO configuration. 3V3/universal cards only.
The main problem was the drivers, but you could keep the prometheus memory map and use their drivers.
Anyhow, I prefer to enhance the main card and not worry too much about legacy stuff for now.
/MikeJ