There's definitely a wide spectrum here. I would say that a majority of "ensemble shows" still have a lead, and/or actors have more prominent parts than others. Or even if the stage-time is the same for everybody, there are characters who are highlighted in the story more prominently than others. Even a Chorus Line has Cassie, even Spelling Bee has Olive, even Angels in America has Prior, even Godspell has Jesus, even Cats has Grizabella, and so on and so forth. Then you have shows like, say, The 39 Steps, where all 4 tracks have equal time in the spotlight, but there's still one actor who plays the protagonist of the story. So from a storytelling perspective, he's still the "lead."
As far as musicals go, I think that Six and Come From Away are two of the "purest" examples of ensemble shows, as described the the OP: "where all actors have equal prominence, whether that means they're all leads or they're all supporting." But I think this degree of "purity" in an ensemble show is pretty rare: most of the time, you still have some roles that are more prominent than others, even if they're all onstage for the whole time.
But for what it's worth, here are some other shows that I would classify as "pure" ensemble shows, as described by the OP (I'm counting 3-handers, but not 2-handers, because most 2-person plays have equally-sized parts, but that doesn't feel like it's in the spirit of this thread):
--The Children
--The Humans
--Ain't No Mo'
--Describe the Night
--Days of Rage
--The Antipodes
--Ghost Quartet (though the 2 women are arguable more important to the story than the 2 men)
--Miles For Mary (and Mrs Murray's Menagerie, by the same group)
--One Night in Miami
--Songs For a New World
--Assassins comes pretty damn close, but you could kind of make a case that Booth is a bit more central than the others.