Nah, not really.

My friend is traveling as seaman status (he'll be joining a tanker vessel in one of the ports in Portugal), and he has an agent over there in Portugal to arrange these "On-arrival Schengen visa" once he reaches Lisbon airport.

As for Bangkok airport and the plane in Bangkok, the agent will give the "Ok to Board" to the airline for his smooth boarding.

If there's no "Ok to Board", yes, then as you said, he won't be able to get onboard the plane in Bangkok.

Anyway, I wonder why the heck are most airlines so unfair to citizens from certain countries like Myanmar? You need like plenty of documents and proof and all that crap, while people from other richer countries can transit any airport with just a single passport.

It's not like Myanmar people are terrorists or anything. If it's some suspicious looking guy from the Middle East, I can understand.