Nice way I have been using:
1. Make a circle shaped backing plate out of 1/4" thick scrap fiberglass (top side smooth)or G10 with a close fit over the through hull. Clean the hull around the hole. My favorite tool is "sponge wheel" 3M makes "paint stripper" tool that is used with drill
motor, a very coarse sponge abrassive.
2. wrap the threads of the through hull with teflon tape
3. mix microbaloons or a filler as recommended in previous posts with epoxy of your choice to peanut butter consistency.
4. stick the through hull through the hull, have someone hold it from outside, preferably with a flat piece of iron that engages the nubs inside to keep it from turning.
5. spread the mush on the hull and the backing plate disc, preferably without getting it on the threads
6. plop the backing plate over the though hull, while someone is holding it on the outside and slowly and carefully start tightening the nut over it by hand until the mush squeezes out evenly, keeping the backing plate flat against the nut. Ideally, you would stop before the backing plate touches the hull at some high spot. A dry test run (without the mush) might be a good idea first if the area is really uneven, so you see how far it can go. If the backing plate tips, because you hit some high spot on the hull, you went too far.
7.
Beer.
8. Next day, remove and rebed through hull with your favourite caulking.