It's not a faith thing. Yes, metabolic advantage is a thing and useless adaptations can get eliminated over time (it seems to matter more in single-cellular organisms, though). However, often enough, unused adaptations can persist for a long time - for example, pythons still have the whole blueprint for "a leg with intricate mechanical abilities" and nerves and stuff, it's literally just switched off. We know because some researchers figured out how to flip it back on, and behold, snakes grew their legs back. That's what I've been alluding to in the prior comment - genes aren't encoding a flat blueprint, but a complex program with many genes working as flow control or signalling superstructure, able to toggle or modify whole complex body parts.