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We repair similar defects daily in the process of prepping our live edge slabs.
For the holes, simply use epoxy with black colorants. Since you can't hide them, make them obvious. We do this all the time with no problems.
For the crack shown in your first picture: This defect is usually caused by kiln drying damage and penetrates deeply. You could be pouring epoxy down that crack all day. Here's what we do:
1. Slice a thin wedge on the bandsaw, angling the wood so that the grain that shows will match the wood.
2. Drive the wedge under and into the crack, i.e. going diagonally into the wood.
3. Go to any store that sells artist supplies and ask for Mixol pigments, they mix very well with epoxy. Pick the color that most closely matches the final color of the wood (after finishing). These little bottles cost about $6 each.
4. Use the colored epoxy to glue in your wedge and liberally spread it all around the edges of your repair
5. After the epoxy cures, sand down your repair. Because the epoxy is close in color to the repair, the area will now look like a natural variation in the wood. The wedge prevents the epoxy from diffusing down the crack into the wood.
We salvaged many, many thousands of dollars worth of natural edge slabs using this and similar techniques. It's kind of tedious the first time you do it, but goes very quickly after that.