Will I face entry denial in Thailand with a South African passport after multiple short visits from Phnom Penh?

My sister arrived on Saturday, it was her fourth visa exemption entry this year. Previously she never stayed more than two weeks and never did any extension. She went through immigration very easily. They didn't ask for anything. No cash, no proof of onward travel, no proof of accomodation were asked. Just stamped and let her through

Not a worry IMO. Enjoy.

An METV is something you would have had to apply for from your home country anyway, so it is not really relevant at this stage. Based on what you describe, three prior entries and a total stay of only around 45–50 days over 12 months is well within what is normally regarded as ordinary tourism under the Visa exemption system itself. That kind of travel pattern is not what the new formalised guidelines are aimed at either. As always, the final decision rests with the immigration officer you meet, and you should be prepared to show an onward ticket and accommodation details if asked. With such short stays on each visit, entering again by air from Phnom Penh would normally not be an issue.

If each entry was only 10-20 days, it's probably fine. Just make sure you have the 3 proofs (cash, onward travel, lodging booking).