I'll add something I find pernicious about this practice.
When you book a truly "direct" flight, you have reasonable assurance about a misconnect. If the plane you come in on is the one you go out on, you can't miss the plane. (Well, you could if it's really delayed and they bring out a new plans, but that's pretty rare.)
However, with these "Change of equipment" flights, you don't even get that. They will not hesitate to have the continuation of US987 go out before the first leg of US987 has arrived!
But yes, customs should be fairly painless. You'll pick up your bags on one belt, go through customs/immigration, then put them back on another belt.