I use every time. 6 minutes last week from plane to taxi !

It will class as an overstay I believe and you'll get a fine as well as having trouble getting back into Thailand in the future.

Personally I would fly out of the country on a cheap flight before your 90 days expire and then come back on a connecting flight to meet your original flight.

You could try and fly out and back again next day and get another 60 day visa exemption but you risk a refusal or questions asked at immigration.