that far out, the airline will try to get bookings for the higher fares for pax eager to by early, when those fares does not sell well at an expected time frame, then fares will start dropping, and once they start selling lower fares, then they will start going up again,,,all programmed like this in advance. had the pleasure of working in that field for 40 years in the USA,,,
i've had a green card for 43 years and never heard of this. and i recently retired with over 35 years for a major US carrier, and if you were leaving the USA then there is no reason to be stopped if you have the valid passport for the destination Thailand. very very strange.
Ask agent at origin if the 2 airlines in question have an interline baggage agreement, if they do, show her your confirmed itinerary and she should be able to tag them thru. Good luck..
talk about other countries getting the same 90 days exempt as well, but those countries must also open up for Thai citizens as well, sadly most westernized countries are still not doing that, it's virtually "impossible" for thai's to come to USA, especially if you are a single woman,,,,time will tell!