Im having a brain meltdown, im not really sure about this so Id figure asking is the best bet.

If I add new creature formids to the player faction (a native faction) in the GECK, does that constitute a potential compatability problem if another mod wants to specify what formids are in the player faction as well?

At first I thought no - it would be fine, but not im not so sure...

Nope, the faction just shows 'use info' on its screen, really. It doesn't hold details of who's in it.

Ah great, thanks talkie, one less thing to worry about.