What I said is that if she only shows her US passport with no visa stamp and she's been staying here for 4 years, immigration would consider her an overstayer. She'll need to exit Thailand with the same passport she entered with
If you entered Thailand with your Thai passport, you need to exit with it, if you exit with your US passport, you have been overstaying for 4 years 😉
Unfortunately there is still no option for same sex couple visa, but it seems that they are discussing it. From that to when it will became reality is still an unknown factor, if ever.