Green card holders must not reside outside the US more than 1 year, unless they have applied for a reentry before their trip aboard. If she is denied the entry, she needs to reinstate her green card first while in Thailand.
if approved, your 90 days starts from date of the application. Yes you would lose many days. Also if approved, they will keep your application for 15-16 days,then you have to come for the second time to actually get the non/o stamp on your passport.
Same day procedure, available thru an agent I guess. ( In BKK office)
If you plan to extend your non/o based on retirement, or changing from your 60 day tourist/ 30 day visa exempt to a non/o for future retirement extention , then yes. Your bank teller can do all 3 letters at the same time, at the same counter. Easy.