This interoperability problem is common among modding communities. The best way (that I know of) around it is corroboration between modders. If two girl makers have worked out the bugs between each others girls and core traits, then the download lists will say so. If, say, a mod becomes so popular that almost everyone uses it, then the best modders will work around that one if they want to get their stufff out there. The human system kinda works out the kinks itself.
As far as mechanics go, I'm gonna keep my mouth shut and leave that to people whose business it is to figure that out; I'm programming retarded.