Re: why you have levels in permissions?
Grouping the permissions into levels was done as a convenience, I think. Originally there were no levels, just a long list of permissions grouped according to Tiki feature. The levels may save the admin from a lot of individual-perm clicking. Of course if you don't agree with how a perm is placed in a level, you can delete it from the level.
I don't know if the permissions docs goes into detail about changing levels and perms; if not, it should.
-- Gary