When I have the 'auto-equip armor' option enabled non-vanilla armor doesn't get equipped. I tried adding them to the item tree, but that didn't work.

It probably doesn't work well with modded armor because I don't see a generic way to get the armor level info, which is what it uses for finding the 'best' armor.

You could make it use the item tree and just hardcode what armor is best. That way people can add their own armor and in what order it should be equipped.