I often fill gaps with sanding-dust thickened epoxy. As stated elsewhere, cured epoxy is hard to sand and will create staining of the surrounding wood. The solution to this is to do the filling immediately before glassing and wetting out the glass with epoxy.

I will mask often mask around the gap with masking tape to keep the epoxy filler off of the strip faces. When the gaps are filled, I peel the tape, lay the glass and wet it out. Since the filler is still soft, it doesn't cause rough spots or present bonding issues. If resin does get on the strips, it is followed by more wet resin and staining does not occur.

For sanding dust, I clean out my vacuum before starting the sanding so there is nothing else in it. After sanding the outside, I have a good pile of fine, clean dust well suited for filler. When mixed with epoxy it will be darker than the sam wood it was sanded from. Adding silica or cellulose to it will lighten it up a bit.

Obviously, this only works if you are working fairly fast. If you want to take your time, some of the other solutions are probably better.