That depends on your immigration office. Most allow when you have 30 days or less left. Some allow 45 days or less left, including the larger offices like Bangkok, Phuket and Chiang Mai.
She can travel on whatever passport she wants, but she should enter Thailand as a Thai citizen using her Thai passport.
If she enters Thailand using a foreign passport, then she is a foreigner as far as immigration law is concerned. The difference is that instead of the 30-day extension, she can apply for a 1-year Thai citizen extension.
There is no US bank branch in Thailand. They are either different entities completely, even if they have the same name, or they are clearing houses and not actual customer banks.
An agency wouldn't have anything to do with the OX visa. There wouldn't be any customers. People get non-O and non-OA. And if you are looking for a long-term visa, why not look into the LTR visa? Much better than the OX visa if you qualify.