Welcome to the Forum.

I've not heard of the agreement you mention between the U.S. and France. It took quite some digging to find a
reference to it. However, that's what France does and they don't speak for the whole of Shengen.
As an American, I doubt they'll bother you too much. But to answer your questions:
1. The Swiss might ask questions, as it would be clear you overstayed your visa. Did you at least leave Switzerland by the 90 days? As long as you left Switzerland and were relying on the agreement with France then I think you could plead your case.
2. I doubt it, but you never know. Sometimes the officers are in a bad mood. I was on vacation when my permit expired (new one was already in the works). When I arrived at immigration, the officer was rather nasty and said she could see in the computer system that the new permit had been issued, but that
technically since I didn't have it in my possession I could be denied entry. If the Swiss border officer wants to be nasty, you could be turned away.
3. I don't know for sure but I'd assume it's mandatory because visas have an expiration date. At the very least one should notify the authorities that he or she is likely to overstay due to the pandemic and ask for guidance on how to proceed. Get something in writing if possible.
Be sure to follow the quarantine rules once you arrive or you could be in for a massive fine.

If you can't isolate in a room separate from your boyfriend, then he has to quarantine too.