So it's not cause Sams doesn't know the playbook but more that the coaching staff can't trust him to execute it, as in, not defer to himself, hold the ball incorrectly, or whatever the hell the staff deems as risky.
This is my guess. He's in his third year, with the same staff, in the same offense. He gets the playbook, that's not an issue. What he does, which is the double-edge sword, is engage in risky plays that so far have paid off huge, but at some point will not and as risk-averse as Snyder is I can see why he would go with Waters.. Waters=safe bet that doesn't fit our offense. Sams=somewhat risky bet that pays off big. Just my guess.