I hope the Phfor Slaving hegemony contacts the Covenant and reforms both groups. (I'm aware of the impossibility of this)

I'm failing to see how any of this has to do with the topic at hand.

We know this for a fact. Prior to the activation of the Halos, the galaxy was inhabited by numerous species who were seeded by the Precursors - many of which we know were cast down by the Forerunners and stripped of any capacity for self-defence to ensure they would never be a threat to their rule, as the Librarian tells the Didact in Halo 3's Terminals. I'd wager that there are still a good number of species that we've not seen yet, certainly we might expect to see some of those that were cut from CE and 2 at some point - such as the Drinol, which would be awesome.

That is still vague. I am going to assume you are asking if the Covenant couldn't have been fighting another empire. The original canon implied that but we now have a retcon. Silentium shows a sizable percentage of the galactic species being destroyed with the greater ark. Those on the Lesser ark were only a few hundred if thousand of the original sample. Which is why we don't see aliens left and right in the universe. 100,000 years isn't enough time to recover.

I don't mean indigenous species, but rather entire empires of other creatures (think another Covenant)

We know for a fact there are after the CEA Terminals and description of the map Wreckage in the Halo 4 EVG.