Do we have the ability to...
Sadly, no, you can't do that. The closest you could come is having said Boss/EB/AV spawn as an ally or hostage after you defeat it, and that won't really give the same impression (it would play like some sort of 'friendly clone' of the defeated boss suddenly showed up somewhere else in the mission).
M.A. Arcs
Intended for high level play: The Primus Trilogy (Arc #s 10931, 283821, 283825), "Freakshow U" (Arc #189073), Purification (Arc #352381, Dev's Choice! )
Intended for low level play: "Learning the Ropes" (Arc #100304), "Cracking Skulls" (Arc #115935), "The Lazarus Project" (Arc #124906)
...make a Boss/EB/AV surrender near the end of a fight, like Trapdoor and the Honoree do in the Alpha Slot arc?
I know we can have them flee, but can they be made untargetable?
(Sometimes, I wish there could be a Dev thumbs up button for quality posts, because you pretty much nailed it.) -- Ghost Falcon