Bruce and the rest of the BB crew spent a significant portion of their time in Bangkok, and of course there are bucket loads of Muay Thai organizations and demonstrations there.
It is not known if Bruce was also exposed to MT in Pak Chong, or if the mythical match actually took place there, but considering it's more remote location and being only a fraction in density and geography compared to Bangkok, I'd wager that the MT practitioners carried on with their fighting without any protective gear or pads.
As for the Muay Thai vs. Kung Fu debate, they're both vastly different systems so I don't feel it's fair to compare them with each other. Regardless, Michael Chan Wai-man (http://www.network54.com/Forum/256969/message/1422646755/Interview+of+Michael+Chan+Wai-Man+on+Bruce+Lee) believes that, if Bruce had faced off the Muay Thai fighters without rules and regulations, he would've easily trounced them.
"Q12: How do you think Bruce’s fighting ability with the Muay Thai fighters?
A: No doubt Bruce should be the best in Southeast Asia then. If fighting in the ring with the Muay Thai fighter, it is hard to say who will win because of the rules and regulations but if it is on the street with no rules and all out, I’ll bet on Bruce, Bruce will definitely win for sure!"