Maybe Zeta Halo is imprisoning a bunch of alien species and the Endless being the strongest of the inmates? The Silent Auditorium was probably meant for more than just the Endless. The Harbinger could be one of the other alien species. If the Endless are as dangerous as some characters make them out to be, it would be pretty underwhelming if Chief just started gunning them down with ease. Maybe in the next campaign, we'll fight a coalition of all the freed species.
Fairly certain I heard Harbinger drop a "we" in one of her lines, implying she's Endless.
So are the endless the precursors/flood, or just another species that were punished like the humans, but by imprisonment instead of having their technology reset?
They aren't Precursors/Flood, there are a few tells. 1) cortana references them as being worse than Flood
2) They survived the Halo array firing somehow, don't think even Precursors would survive based on the space magic explanation of what the Halos do (they target nervous systems/neural physics, which is foundation of Precursor/Flood existence). The Endless were imprisoned by what remained of Forerunners/Forerunner AI some decades after the Halos fired.
And personally I think they would leave at least one hint that they actually were Precursors. Otherwise it sounds like writers are going out of their way to tell audience these are something different. Writers are clearly focusing on 'time' as a trait associated with Endless, too, which isn't really the definition trait of any other Halo species