My husband has a Philippines passport and a USA passport. The Philippines passport is just about worthless outside of ASEAN, but it is rather beneficial for ASEAN countries that require visas for USA citizens.  The problem is that we are flying into BKK from USA via Japan, so he will definitely need to arrive in BKK with the USA passport.  We have a separate flight booked from BKK to RGN. Will there be any issues with leaving BKK with the USA passport and entering RGN with the PI passport (Thai Smile)?  We will be reentering Thailand via a land crossing in Kawthaung.  We will only be in Thailand for a few days before and after Myanmar.  I guess another option is to try to enter BKK from Japan with PI passport, but I would imagine that would be even more problematic since the flight data would show a USA passport for him.  Ideally, he would only use the PI passport for the entrance and exit of Myanmar.

Your husband can enter Thailand using either US or PI passports. A passport showing at an airline check-in counter can be different from the one you pass through the immigration check point for departure/arrival. However,  you must use the same passport on which you enter, to leave the country.  

There has never been an issue about the flight data conflict.  I hold Thai and Australian passports. When I return to Thailand from Australia I use the Australian passport to check in (my flight data record as I am an Aussie)  but when I arrive in Thailand I use the Thai passport to pass the immigration so I can stay in the country indefinitely. (If I enter as an Australian I can stay up to 30 days). On the other hard, when I leave Thailand to go to Australia or go other countries where there is no visa requirement for the Australian passport, I use the Australia passport at the check-in counter to show that I can travel to the destination country and  then use my Thai passport passing the Thai immigration.