So, this is a thing that's always kind of confused me about caster PRCs anyway. Take Mystical Theurge for example, you start down that dual path at about 6th level, with 2nd-level arcane and divine magic. Based on how I'm reading the class description, you never gain new spell *levels*, just more spells per day in the levels you already have. Why would you even do that, if that's the case? How are PRCs handled in T+? I'm almost done with Co8 NC and planning to start a KotB campaign focused on taking PRCs, and want to know if it is worth it to do that, or just go with some of my more non-standard class choices (I never play paladin, monk, ranger, barbarian).
KoTB is a module designed for low level characters. I think you may be able to reach 8th level if your party is small enough, so I doubt PRC's will come into play.
Technically, when you level as a Mystic Theurge, you gain spells as though you leveled both your casting classes chosen. A 5 Cleric/5 Wizard/10 Mystic Theurge will have access to 8th-level spells, both Arcane and Divine. A 10 Cleric/10 Wizard will only have up 5th-level spells. As for Prestige classes in Temple+, I haven't played around with them yet, I imagine they should work no differently from multi-classing, except for the fact you get around the EXP penalties due to how they work. However, as mentioned though, KotB is a low-level campaign, its generally not a good idea to play around with Prestige classes unless you know your characters are going to hit level 10 or higher. Especially as a Mystic Theurge, since until you're able to get levels in Mystic Theurge, your character is going to be an absolutely terrible caster at both Arcane and Divine. Being stuck with only 1st and 2nd level spells, while everyone else is casting 3rd and 4th level spells. Personally I hate Mystic Theurge. I think its a terrible class, and is a trap for players. I think I mentioned somewhere, that in a campaign I was GMing the only casters in my group were a Bard and a Mystic Theurge. I had to tweak so many encounters, because the MT was so horribly underpowered for such a long time.