The property owner is required to file a TM30 any time a foreigner is staying at their property. No exception for the METV. In practice many condo owners renting on airbnb and similar sites never file TM30s, and many people are staying in these with few if any problems.
I have extended visa exempt entries many times in Phuket at the main office in Phuket town, and they never asked me for a TM30, and I am sure a TM30 was never filed for me. I would recommend trying to extend without the TM30 a couple of weeks early, and then worrying about filing it if they ask for it.