> Does that mean in the MorphOS world that every combination of
> motherboard & video card is supported or only some combinations?

There are compatibility restrictions like slot type, voltage, BIOS type, presence of bridge chip etc.

> I would like to run MorphOS on both the Sam and X5000 and am trying
> to find a card that is supported by all OSes I'm wanting to try.

Regarding X5000: not yet supported by MorphOS. Wait for 3.10 and see what will have changed in terms of graphics card support.
Regarding Sam460: Use an R500-based Radeon (X1300 to X1950). R500 is well supported by MorphOS (including 3D) and mediocrely supported by OS4 (including Compositing, but no 3D).