How are you sanding it down? Are you using an orbital sander which is always best? If not, and you are sanding by hand, always use a sanding block or else your fingers will influence the finish. (you probably already know all that).
I've painted a lot of cars over the years, and each car is different from the last car. Part of the problem here is that the filler has very different properties to the fiberglass and so you will often see the imperfections when you paint it due to the different surfaces etc. I would fill the logo's with fiberglass because then you are sticking to the same materials. If you want to go extreme, cut the GT4 logo out, fill the gap with fibreglass and mesh and flatten if off.
If you wrap them, the logo may still show through as wrap is extremely thin. I wrapped a mini a few months ago and I couldn't believe that all the shopping trolley dings still showed through the wrap.