I can speak from recent experience that this is likely to be a problem. If a Thai national born in Thailand enters or leaves the Kingdom then Thai immigration law states that they must use a Thai passport to do so.
On our recent trip to Thailand we experienced a problem with immigration when leaving. Fon's Thai passport had expired and Thai immigration had asked to see it when entering after she confirmed she was Thai when asked - even though she presented a British passport. Unbeknown to us they added a note under the entry stamp in the expired Thai passport stating that it must be renewed in Thailand - although the immigration officer didn't say it HAD to be done We were hoping to get it done up in Khon Kaen but due to the Songkran closedown and various other commitments we didn't have time to sort it before leaving for home. It's ok I thought she has a valid British one and will renew the Thai one back in the uk when sorting out a Thai passport for our daughter. Big mistake! Checked in ok at the airport using valid British passport - seats allocated and bags on their way, security passed only to find that Thai immigration stopped us asking where the new Thai passport was? They then refused to let Fon leave until she had a valid Thai passport even though she had a valid British passport as "she is Thai" So we get bumped off the flight and have to find a hotel and wait until the passport office opens on Monday morning. New passport picked up Wednesday morning and get back to the UK five days late (boss not pleased!)
So the moral of the story is to use the Thai passport if your stepson was born in Thailand. If you lie to immigration and state that he was born in the UK you are likely to come a cropper IMHO as the place of birth is clearly indicated.
A costly mistake for us and probably additional costs for changing flights etc not covered by travel insurance.
Do what you feel is right for you but I personally wouldn't take any chances with Thai immigration as they are really on the ball.