Yep, part of the fun was supposed to be in figuring things out. Also for thematic reasons, as I just explained in reply to earthfarers comment. As in, Apprentice is only one acting in faith, and therefore he encounters things forgotten/ignored, and has to figure out how those things work, since there is no one to instruct him (except what he read from the book)
there was actually supposed to be a big boss in the game too, already had generated graphics for it, but didnt have time to add it. Idea was that it had been this big black thing that sucks colors, and then you would have needed to damage it with all 3 colors, as in, it would have had separate health for each color. That you couldnt destroy it by just using red, but had to use all red, green, and blue to beat it.
It had been like a final attack to try prevent light coming to world.