I am the OP.
I just stumbled upon the great news that the MorphOS bug preventing a 2nd PCI-E GPU being used has been fixed in 3.17.
Thank you to the developers for fixing this. Now I can have the best of both worlds.
I will be looking for a 1950 XT for MOS to complement the 580 for AOS41.
The 1950 will fit in the Define 7's vertical GPU slot, and with riser should not block other AIC slots on the 5000 motherboard.

I will say my perception from this experience is some of the MOS team comes across as hyper sensitive cry babies. Instead of getting angry at users asking questions and blaming others but not looking in the mirror until now is really sad. Luckily this MOS bug has been fixed and I am personally grateful to the developer(s) who fixed this. Was the bug more complicated than hardcoded expectation of the display adapter being in the x16 slot? Without sources I will never know, but regardless now all x5000 owners in my shoes can now use MorphOS. Well done to whomever fixed it.