What you don't see are the hollows that your sander is making right under your nose. The varnish will reveal a nicely rippled and uneven surface. The bow of the Expedition. The dark Western Red cedar and Redwood were filled carefully so that the filler would not contaminate the pine and the light wood. Water based fillers are the most forgiving of mistakes and can be used right up to the fiberglass work.
Epoxy fillers are the worst by far.
If you want to use epoxy putty you might as well seal the entire surface first with epoxy, then use the putty, and then sand the whole thing before glassing. It is simply too much work for little return. The whitish haze left after this filler completely disappears under the epoxy resin. Most other fillers are NOT that forgiving and you will have to sand the stuff out of the wood. Both Oil based fillers as well as epoxy filler, will leave a distinct spot of different hue if left on.