The first thirty minutes of shop time I've had in 6 weeks was spent reviewing the pews. It gave me an opportunity to see the results of various filling experiments I tried on the project. (Of course it's recommended do technique 'experiments' on scraps prior to the actual project, but this time it's on the project.)
The first 'filling' job was the plugs to cover the screws. Made with the Veritas Snug Plug cutters from Indian Ebony these proved to be highly successful. (But ebony is not cheap). The plugs simply tap into to place and hold with glue. To finish simply flush trim and sand.
The first Epoxy experiment was done using the west system microfiber system. The microfiber in fine powder forms acts to thicken the glue and allow better filling properties. However, this also tinges the filler white... not such a good look.
Next up with have microfiber with fine saw dust. Allow I've had success with this technique in the past this time it made the filler appear heterogenous (ie. tinged white with flecks of reddy brown). Better but not there yet.
My final option was black oxide. This carbon like powder is designed to colour concrete and is dirt cheap. Used with or without microfiber it made a solid homogeous filling agent. Perfect... well if your wanted black any way.
Defects that were exposed to the element while the tree was standing often have a black edge. I presume this is related to oxidation within the wood. Filling these gaps with black filler is effective.
For other colours, such as to match the reddy brown, I would try even finer saw dust (such as that out of the sander) or turn to dyes and stains to turn that white tinge what ever tinge you want.
Epoxy has a significant advantage over water based fillers such as 'putty' - strength. Epoxy can seep into the defect, completely fill it, then set harder than wood, holding the defect together. This strength is essential to fill large defects and stablise burls.