Congrats on building your Spacewalker, not too many kit builders left anymore. I wouldn't worry to much about the seams as a full scale fabric covered plane also has very visible seams, especially on areas reinforced with pinking tape, for example. Careful sanding the covering as your likely to go thru the primer and start raising the fibers which will then need to be pasted back down with some sort of adhesive. For what it's worth, I've built many kits and always left the seams alone. My only suggestion (for the next project) is to plan your covering layout in a manner that places the seams in less visible places (as you've already done on the fuse bottom).

If you're dead-set on touching up the seams, I think light-weight spackle is the way to go. Apply very little and use an old credit card to scrape most of it way only leaving enuf to cover the step on the seam. Then VERY carefully sand with 400 grit to feather it into the covering. As there is a very good chance you'll sand thru the primer (not good), perhaps you want to practice on a test piece?? Anyway, good luck finishing up your build and remember that if someone can see the seems on the plane, they are probably standing to close!!