Question said:
Theres also the "issue" of how the level 20 wizard can get stumped on a simple knowledge roll, while his apprentice knows everything about it.
That's only an issue if the wizard starts play level 20. You don't have to make Knowledge rolls for what you already know, for instance.
EXAMPLE OF WRONG
GM: The green-skinned giant advances, leering with jagged teeth and mighty claws.
Wizard: I ready a scorching ray.
GM: Make a Knowledge (nature) check.
Wizard: Why?
GM: To see if you recognize the creature.
Wizard: But I do recognize the creature. It's a troll.
GM: We'll just see about that. Make a knowledge (nature) check.
Wizard: Well, if it's knowledge (nature), it must be a giant, and if it's green, it must be a troll.
GM: You don't know that.
Wizard: I don't even know what kind of check I'm making?
AFAIAC, by the RAW and the examples of play given in the book, I am free to metamage knowledge of monsters if I think it's reasonabe for my character. Knowledge checks deliver new information. They are not a requirement to simply know something.