I'm not sure how these depth issues relate entirely to tempo. If the offense is to play fast then the entire offense should be playing fast ... in practice, in scrimmages and in games.
The drop off in depth at RB, WR, OL has nothing to do relatively speaking with the ability to play with tempo. For example I suspect Kade Warner and Reimers is capable of rushing to the LOS and running the next called play regardless of their ability. Ozigbo and Washington were the two primary RBs ... how does a drop off in talent prevent them from rushing to the line and running the next called play?
Having an inexperienced QB ... yes. Sometimes AM needs to tell the huddle we are going to play fast - cue to me. Snap the ball early, get offside penalties, substitution penalties ... as AM et al get more comfortable, I suspect SF and company will give them wider berth.