Board Thread:Warhammer 40k General Discussion/@comment-25618639-20150807010020/@comment-27561619-20160205031320

It is also possible that the Emperor made a bargain with other "Gods" because 'a realm of immortal gods' doesn't definitively say Chaos Gods or does it.

The Eldar Pantheon is mostly dead but who is to say that some of the lessor deities didn't escape death or capture.

Then there are the Old Ones who made the Webway gates (hint hint) and created (hint hint) the Eldar and quite possibly the Orks.