I think your title is a little misleading. You just didn't realize the system until too late. Yes, if you had left from Gate 2 domestic, you probably would have not had any issues at all. You would just have returned to the airport and had to process through immigration in BKK at that point, and no-one the wiser. And you would not have had to pay another departure fee, which was already included in your ticket. You could have also at the outset in USM, just had them check you to BKK and tell them you'd do the final segment check-in in BKK.

I actually do this on layovers in Bangkok all the time, if I have over 7 hours. No way I'm staying around the airport. I've never had any issues doing this. This also works on intl-to-intl connections in BKK, such as PEK-BKK-LAX which are now really long (22 hours including an overnight). I've been known to tell the check-in desk at my origination to ONLY tag my bags as far as BKK, not to the final destination, and that I'll pick up there and recheck myself again. Typically, I'll get a new boarding pass issued in BKK even if I already had one. Usually, I don't even get tagged for the 700 baht exit fee--my success rate at avoiding this on the intl-intl connection with "stealth" stopover is about 75%.