I've seen boats run with the gap between the transom and saddle unfilled. If the transom is strong enough to support the motor and thrust, it should do so with the motor raised up a bit as well. Especially so if you're using the same bolt holes.
I would, however, think that if that gap was excessive, and you had holes closer to the top of the transom, you would want to structurally raise the transom height (not just fill it, but make it structurally sound.)
FWIW, West Marine does one thing pretty well: post sale support. Might give them a call.
From the US:
Phone: 1 800 Boating (800) 262-8464
Fax: (831) 761-4421