We're talking about a person that stay in Thailand and just before the 60 days expire (for example: 1 day before) he goes and use the other 30 days left.
It's in the visa.
The count of the MAX 3 months extention has been activated on the TRANSIT VISA (VOA= Visa On Arrival).
But in this case it's not valid as you have REAL VISA on your passport.
By the way,as far as I know,the rule of the 30 days visa stamp on arrival is only in Bangkok / Suvarnabhumi airport, when crossing the border by land you get 15 days VOA and NO LIMIT.
This information taken from a police officer in Kap Chong Surin border 2 months ago and from internet search.