CA glue works OK for hairline cracks, but for larger voids, the only way to go is epoxy. Then you can add all kinds of colorant. I work with mesquite and when you get logs of that it often has been subject to prairie or deliberate fires to control it, or water stress cracks that eventually fill with minerals. These dark lines when exposed can be scraped with a knife blade to provide a perfect colorant for darker voids. Coffee grounds, but I grind them finer with a mortise and pestal (dont tell the wife), super fine sawdust of different types of woods etc. Another trick is to make two different colorant epoxy mixtures, one say out of burn mesquite or walnut, another out of india ink or mahagoney and epoxy, apply some of each to the void, then using a stiff wire or dental pick, do a quick swirl or two or three in the void. You dont want a complete mix, you want it swirled, looking more organic than just a single color, so it appears as natural. This works well when you have an area larger than say 1/2 inch dia.
Practice on a piece before you move to the main event.