Depending on the size, there are hot glue gun type products that can work well to fill smaller stuff, but the bigger stuff is resin country.

You could also use sawdust and resin or wood glue to fill holes if the black resin doesn't jive.

Keep in mind that each one of those options can't necessarily be sanded and finished the same, so take that into consideration.

Total Boat is great. It keeps up with West System Epoxy, and it's cheaper. Also, Total Boat allows you to thin with acetone per the instructions. Total Boat isn't picky about what you put in it. Use some black wood dust or take your pick of dyes, even the Ritt dyes from your local supermarket should work just fine.

I have done pretty much exactly this very recently.

For some knot holes and cracks in the tops of the walnut cabinets I've recently posted about, I used System3 Mirrorcast. It's a 2:1 volume mix, it comes in a 1.5 quart size, and it's a crystal clear casting resin "Designed to fill knots, cracks and voids with minimal shrinkage." Freshly mixed it has the viscosity of maple syrup or so, maybe a little thinner, it will self-level, and wicks into cracks.

I dyed mine black using their CastFX colorant which is designed specifically for their casting resins. In the pot it looked a little translucent but once in the wood it's just inky black, looks great against the walnut.

The one downside it has, it takes forever to cure. The TDS claims a 1 hour working time and I think it's actually longer. It takes 7 days to fully cure, and it remains thin and flowing for several hours after the pour. It can wick into wood.

If you can get a paintbrush into the void you're filling, I suggest mixing a small batch, waiting a good 15 to 30 minutes, then painting it on the surfaces of the void to be filled. Let that cure for a good 12 to 24 hours, and then doing the full pour. Again, when doing the full pour, mix up the batch, and then just let it sit in the pot for half an hour.

Make sure the upper surface of the board is level to gravity. Pour it so that it just slightly protrudes above the surface under surface tension. A cabinet scraper is about the best tool for leveling it with the surface once it's cured. As you sand it, it'll take on a grey scratchy appearance, but it'll look clear (or black) again when you apply finish. I can confirm it urethanes well.