The receivers all run crossing routes or go routes, or posts/flags... Did you notice the only comeback route run was when Trace was qb?
They can't run double moves because the line does not hold up long enough, AND, Lamar rarely throws a comeback route. So db's can sit on crossing routes, keep the safeties in the middle part of the field and single cover on the outside.
All of that limits the plays, the route combinations that can be run thus stunting Lamar's numbers and the momentum of the game; quick strikes.
Allen gets to throw those routes, which gives his receivers an advantage with the double move available. He is accurate enough so his numbers go up, especially with those routes he is able to move a safety playing on or outside the numbers, a step or two; big adavantage.
Until Lamar proves that he can throw outside the numbers consistently, he will limit this offense. Right now, Allen has made the biggest improvement and earned his money while Lamar has not to this point.
Baker is slowly coming around, but he has not been consistent enough to warrant the big pay day.
There is a reason no running first qb has ever won a super bowl, Kaep came close but he was helped by the NFL with that power outage.