Phil is correct about alcohol-based leather dyes penetrating most finishes. Ive used Tandy leather dyes, mixed and thinned as necessary, to touch up a variety of furniture and stock finishes and add coloring to streaks of sapwood. The 3-ounce bottles of stock stain/dye sold by Galazan also penetrate finishes well, and are water-based. Both of these product types seem to be least effective at penetrating pure urethane finishes, but work equally well on Tru-oil, lacquer, oil-modified urethane, and shellac. None of them seem to impede the application of additional finish coats, and none that Ive used have done anything peculiar in the long term. Some leather dyes can be very light fugitive, however, and may not be suitable for something exposed to light for long periods.
None of these products rub off on your hands after application and drying, but can be very difficult to apply evenly over large surface areas. Until I had sufficient practice, I ended up stripping a number of dappled stocks back to bare wood and starting all over again.
Gunmans suggestion of ammonia fuming may be an excellent method of darkening the wood, and should penetrate an oil finish. If the stock in question is Walnut, as I assume it to be, it should have significant tannin content and be a good candidate for darkening during the process.
Good luck!