Removing it should not damage it, if you are careful. The gasket itself is not glued in, but grabs onto the rails around the perimiter. I removed mine when I had the car painted, and suggest the same. It will just not come out well taping off, as you will always see where it was taped.
I also bought new tracks from the Fiero Store, as mine were completely rusted out, and just small pieces of the old tracks remained!
Here is a shot of installing the new tracks, as you can see taking the gasket and tracks out to paint, was a much better way to go: