They specifically state that you can multiclass all the base classes you want. You can be a fighter/rogue the first level and a ranger/hexblade the next, if you want (and have the alignment qualifications to match).
The prestige classes, however, were NOT designed with the gestalt rules in mind. It is easy, as in your example, to create situations where the characters would become way too powerful, even for a gestalt character. That would be okay if everyone in the party was totally munched out, but it's utterly unfair if only one character is.
In a Gestalt campaign, you definitely want to carefully consider any PrC before you allow it. But even Mystic Theurge *could* be okay, as long as the character's other class isn't gaining spellcasting levels in the same classes. Say a Mystic Theurge/Dragon Disciple. Disgustingly powerful, yes, but no more so than a barbarian/rogue (raging sneak attacks! Owww!!!!!!)