The knees and elbows are big differences between MT and most kickboxing styles, but not the only ones. MT also uses leg kicks, which are not allowed in all kickboxing orgs, and MT has some limited grappling and throws, which are also generally not allowed in kickboxing.
You are correct that the individual gym will have their own rules.
"In case you ever wondered what it's like to be knocked out, it's like waking up from a nightmare only to discover it wasn't a dream." -Forrest Griffin