I had the same situation for an extension. I had to do the new TM30 first, had to pay a pretty solid fine (1600THB or smth like that for 2month overdue) and after that I was allowed to do the extension. Not exactly the same, but the officer were pretty strict in Jomtien.
Borderrun implies, you come back again? So you are in Thailand for more then 183 days a year? Then you will have to file for taxes. The tax resident status and the visa status are not linked to eachother.