Tod, just out of curiosity. What if she has a multi reentry permit valid until Oct? While exiting on US passport and reentering on her Thai passport will eliminate the overstay issue, her extension of stay will still stay valid until Oct, no?
Long answer is that reentry permit is valid until the current "admitted until" date. So, if you buy a reentry permit before you extend your stay on 3 month non - b, you will have to buy another reentry permit after you extend your visa.
Far as I know, all South Asians have to go back to their home country for any kind of Thai visa unless they hold some sort of residency in the country they are applying.