@Dan ********
, you need to brush up on your terminology for the visa you're on.
That visa doesn't require a 90 day check in<- that is what people on long term extensions do at the immigration office when they're here for 90 days
Your visa only allows you to stay UP TO 90 days then you exit/re-enter the country by 'border bouncing' to get another 90 days.
You have your answer from
@Biff ******
, Mae Sai won't let you bounce out if you can't get back in. When you stamp back in just check and make sure they stamped you in for another 90 days.