most of their song have layers and harmonies, they dont need to reproduce them all live, if they had to, Don't Stay and most of meteora would never be played live. thats not a problem, chester never sung the higher harmony in the bridge of IMR or the outro of Numb exactly like in studio. you are complicating it too much. the only real hard part is the outro with the "screams" that as i said could be done like TLTGYA.
They've used a ton of pre-recorded backing vocals for live performances starting with ATS. Iridescent, Waiting For the End, and Lost in the Echo are the songs with the most substantial use of them, but they also use them for small parts of songs like Burning in the Skies, When They Come For Me, Wretches and Kings, and In My Remains. The vocoder parts on Lies Greed Misery, A Light That Never Comes, and Until It's Gone are also pre-recorded, and Mike sings over the top of the album version vocals on Fallout and The Requiem. That assumes that if Chester's doing the ad-lib part at the end, Mike/Brad/Phoenix would be doing the 3-part harmonies underneath him, and I seriously doubt any of them has the range to hit the highest of those 3 harmony parts in a live setting. You're also assuming that Brad would actually bother doing his vocal parts, as it seems like he does everything he can to get out of singing his backups every night. I've seen videos of Iridescent where he's literally got his mouth closed, but keeping it as close to the microphone as possible so it looks like he's singing if you're looking at him from the stage like the rest of the band is. Mike would probably yell at him otherwise. The thing with all the songs you mentioned though, is those harmony parts are incredibly minor details in the scheme of the whole song. The dense harmonies in Robot Boy are pretty much the defining characteristic of the song. They don't do Robot Boy live for the same reason they stopped doing Hands Held High live, they just couldn't feasibly do it justice in a live setting with the way the vocals are arranged (Mike has publicly stated this was the reason HHH was dropped in 2008).
You gotta envy those who get to be surprised when the band play "Robot Boy" ... although I don't envy the disappointment that they'd feel when it first dawns on them it's just an instrumental interlude