I started with my engine mounted on the transom (there was already a pad fitted) and had problems with mainsheet catching on the motor, or its tiller handle fairly often. I tried a cover, but it made little difference with the engine on the transom. By the way, I sail with a centre mainsheet.
In the end I copied the majority and put the engine on a bracket, and that resolved the problem. The only negative factor is the additional weight leveraged off the back, which does impact boat trim. For me, the loss in performance while cruising is worth the safety factor of having the engine immediately available.
I replaced the plastic pad on the extension with my own (laminated out of ply), because I wanted the mount the shoe as high as possible to ensure it stayed out of the water, while keeping the engine height correct. I’ve also mounted the engine to port, which means that my tiller handle is outboard. Opinion is divided about if that helps avoid snagging; I thought it did. I also mounted the engine far enough to port to allow me to fix the outboard and steer with the rudder.