Yeah, in general kolmafia checks if you equip an outfit and aborts if you don't have all the items, while KoL itself just equips whatever you have and ignores the rest.
Both have their uses: I've been frustrated by kolmafia aborting when I just wanted to equip whatever I had and I have been annoyed at kol for not warning me more clearly after some item got stolen in pvp and I only equipped half the desired outfit as a result.
As it is, it's easy to replicate the kolnative version whenever you want it by simply calling cli_execute("/outfit <name>"), that way it will get passed as a chat command without interference.