I've made many baits using the method you described, in which you wrap the foil over the back and the belly and then trim it off and, yes, it is very common to have it protrude slightly after you clear it no matter what type of foil you choose.
To remedy the problem try this....
First burnish it down as best you can prior to clearing it. I use the handle of an Xacto knife and push down along the seam to flatten them as much as possible first.
If after you apply a coat of clear the edges still protrude a bit, just add another coat of envirotex and they usually disappear completely. This extra coat of epoxy prior to painting will not hurt musky baits at all as far as the action goes since musky baits have much more mass than bass baits.
Here's a few I did a few years back with the same method you described. Note also that just a bit of paint over the seams will cover that line left where the two seams meet on the back and the belly:
This one shows that even with rounded surfaces, which cause the foil to wrinkle a bit and bunch up here and there, you can burnish and cover the protruding area with multiple coats of epoxy prior to painting:
-Vince
fatfingers baits