When you make your reservations, you can ask to have the fact that you need a medical preboard noted on your reservation. Then, when you get to the gate, nicely advice them that your son has a medical condition that makes it a bad idea to be in a crowd, and again ask for medical preboarding. Southwest is the best about this, you can just ask for a blue sleeve, which is their way of symbolizing a medical preboard. They will always take you before the first group. Other airlines are inconsistent and will not always separate out the non-wc medical preboards from other preboards, like first class. It depends on who you get and is unpredicable, although they are supposed to do medical preboards first and separately.
I have a respiratory condition that's set off by standing in the jetway. We think it's a reaction to fuel fumes. If I stand on the jetway, I start choking, so I truly need to preboard so I can move on in a smooth quick motion. We thus ask for the medical preboard (different than a preboard based on age) and then look alert and move into place so we can go first just in case the person boarding blows us off (not an issue with Southwest, who's great about this). This may not be so easy for you, maybe you could camp out by the gate? If you don't need to secure overhead space, boarding last is a good idea, as your son won't have to wait in a crowd.
It can be quite frustrating for us, so here's sending you pixie dust for a smooth trip! It's weird, bc it is in their interest as well as ours to have a smooth boarding, whether it is avoiding dragging me off to get oxygen bc they prevented me from doing what I needed, or issues with your son in a crowd. But they don't seem to see it that way. And I *know* what they have to do, but they still don't do it. They tell you they will, and then do not call me separately. It's very stressful, with the exception of Southwest, who is fabulous. We've had OK luck with American, poor with United.

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