Its pretty simple.
Most kung fu schools do not train at the level modern day MMA and Muay Thai train. Its the reason why I left my Kung Fu school.
I love doing Wing Chun, but I spent the last year watching my school water it down. We used to get our asses kicked in there, it was brutal. Now people complain every time you give them a tap on the face to let them know they got hit. Any because my sifu wants to keep business up, he favors "playing kung fu" over actually do it.
Seriously, how do you expect these guys to hang with muay thai guys? When I think Muay Thai practitioners, I think of some of the most fit athletes. When I think of you average kung fu guy, I think of some out of shape yuppie.
So I would agree that most Muay Thai guys will best the majority of Kung Fu guys. I have only met five people who really do kung fu, even these "Masters" are only "playing" kung fu.