1. Negotiate before with the profs. This sounds cool and I had deadlines shifted around/accommodations made for much worse reasons than this. Maybe pick a class from a prof who already knows and likes your son.
2. Talk to the department. My experience was generally that university administrators erect obstacles while department level bosses help students. If you talk to the dean or the undergraduate coordinator, they may suggest an idea for him or they might reveal the ability to waive policies or otherwise make sweetheart arrangements.
3. Greatest "schedule filler" class I ever took was Math 451 Intro to Topology. This is the least helpful for you (since it is not a good one to miss 3 weeks of and you probably need to be in a math adjacent major), but if you have or almost have the background, I recommend it. It was one of the most mind expanding classes I took. (Part of this had to do with the fact that I was less prepared than the other students and I really had to up my game to keep up.)