my dad has a cover for his that snaps on at the ‘back’ end of the bow plate so he can leave his on. Slightly different than what it sounds like you are planning, my only real issue with his is that he cannot use the stabilizing Ram (unless he gets the cover modified). That would bother me a lot watching the head wobble around the whole trip (terrova).
My cover will not fit without taking the motor off. So I put it on a quick release plate and I have a pie e of foam I put over the base just so it doesn’t try and tear at the cover. Having to take it off doesn’t really bother me, but the boat is always indoors when not in use, so the cover only really goes one for a couple longer trips during season and then at the end of the year when it gets stored at a friend’s shed for the winter. I would say I think having the tm off helps snug the cover tighter.