In regards to the leader menu? It wouldn't be a show stopping issue, but it does raise some issues. Alternatively, I do believe one could 'hardscript' the scenario for a map to set the player's Civ to the theoretical Flood. However, there may be some other UI related issues from adding a new Civ the engine doesn't know about (at the code level, obviously it 'knows' it about at the data level).

Eg, when I added the 'UNSC Scarab', the selection icon no longer used the Scarab's portrait art, and instead defaulted to the generic SoF crest/shield/thing. I'm pretty certain this was due to me changing a specific property from 'Covenant' to 'UNSC' in the copy-pasted UNSC Scarab properties. Not changing that property to UNSC, as I recall, caused some unit train/control issues (I forget what exactly)

: Oh and you mentioned using flood unit(s), were they any good? Or should they
: like I said be 'treated' statistically to be able to level with the
: UNSC/Covie counterparts? IYO

I didn't use or test them in any strategic sense. I only added the train commands to be able to setup controlled scenarios where I could send Flood units against the AI for fine-tuned recording of their interactions.