I'm fortunate that I only did the gauntlet twice; once I was on Air Canada and didn't get a second look (checked in online without issue both ways). The other time I was on United. It took some work in the GS room at ORD (two agents and a phone call) and a note was put in the record for the gate agent (who didn't trust the note and read TIMATIC for himself). But it worked. On the way back, I was able to check in online (with stored passport data) and it wasn't an issue at the gate as I was already pre-cleared and it was contract staff working the gate anyway that was borrowed from Air Canada, I think. I had no issues at the border even though I had commercial goods to declare both ways both times and had to speak to a CBP/CBSA officer in each direction on each trip.

Those were the only two times my passport was out for visas and I had to travel without it. Every other time I have used my passport for airline check-in with United; I use NEXUS card with Air Canada "just because" and they seem setup for that. I recommend using a passport, but that recommendation is no excuse for airlines like United not to step up to the plate and do what is right.