You can go to MY. Day 1 arrival, day 2 submit application (morning), day 3 pick up your visa (afternoon) and fly back to TH (evening). Based on my experience :)
A few question to be clear. I would have to cancel this extension the day I resign from the company (let's say today)? If I do not cancel my work permit and visa extension on that day I am overstaying my visa and will be fined on my way out if I exit (let's say April)? There is no way a I can stay in Thailand legally on that extension/visa if I quit my job without having a new one lined up?