Never fill cracks with wood filler, even if made with wood dust. Problem with wood filler is that it... looks like wood filler. It looks cheap, unloved and you'll always regret every time you look at the repair.
Even imperfectly matched wood looks better. Try oiling a sample of the filler wood to see what colour it will become.
Once you have degreased/de-oiled the base wood, feel free to enlarge the hole to make a proper fit as you don't want to fill a shallow scoop of a hole, then insert the sliver of wood you have prepared - grain in same direction - and glue it in. The better the fit, the better the look. I have fixed floor boards with saw marks across their grain using small slivers sawn off from other boards and it looks great.
Epoxy is a failsafe heat and water resistant glue and it it will bond to remainders of old glues. Does not matter if the epoxy dries clear or brown as your filler piece should perfectly match the hole and so you won't see the colour. Think of it primarily as an adhesive, only secondarily as a filler. Don't use PVA as it does not glue to old PVA and anyway is not that water resistant. Then sand flat and oil etc.
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