I'll use the hand lotion analogy again
When you use hand lotion, you want it to be absorbed into your skin, you don't want globs of white crap on your hand. Same thing with skis. You want it in the base, not ON the base. You iron it into the base, then scrape the excess that doesn't get into the base, off. You don't want to get rid of the wax thats IN the base, which is what base cleaner will do.