@Brandon ***********
People post here already knowing the answer but they just want reassurance and positive answers.
It's her 2nd entry, 3 months is a great amount of time but tourists stay longer than this in Thailand. She stayed 3 months and wants to stay longer it is fine. Returning on the same day is not advised but 3 days and then come back is safe. So if she is refused at the border, small chance but no big deal just bus back to Penang or KL and fly into phuket.