In what way doesn't it support Ware3's mod? I might be wrong, but I reckon only the prefab list would, or might, be at odds with KG's "Generate custom POI's list" - and all that don't comply can be edited, or simply removed if you don't like them. No?
Edit: Just tested my KG-created map which uses a much-edited Vanilla/CP47 poislist, after removing the rgwmixer.xml altogether. The game ran just fine without it, so I have to assume that KingGen's code "poislist.txt" (or whatever name you use) is used by the game in place of the rgwmixer.
I love his map - one of the best I've ever seen, and his prefablist is pretty unique, but does also contain dozens, if not all of the CompoPack prefabs, so it's worth pursuing, and maybe adding them into your own personal prefab list. It's certainly easy enough to cut and move your existing prefabs to a safe spot and then move War3z prefabs in its' place, and then run KG, and generating a poislist..