Ebonizing is a good way to get a dark stain on high tannin woods like oak. It reacts with the tannins and creates a black pigment. It is a different process than what happens in bog oak. The penetration can be shallow to deeper depending on time and if the wood was in a pressure/vacuum tank. The wood is still the same, just darkened to black.
In bog oak ... which can be many woods besides oak ... the submersion in low to zero oxygen water and other anti-bacterial organic compounds in the bog or lake bottom create an environment where the wood does not rot. As it lays there for 100's of years it slowly carbonizes as the lignum breaks down and gets replaced with silica and other minerals. This leaves behind a hard, brittle material that has the cellular/grain structure preserved but the organic structure changed to a mineralized version. As time goes by, the wood changes from the tan color of dead wood to brown in a thousand years or so, and eventually to black by 6000-8000 years. Older wood regularly has silvery streaks of silica that has replaced the lumen and xylem. A hundred thousand more years and it would become petrified completely.
Bonus nerd stuff:
Ebonizing is iron acetate reacting with tannin, which is a phenolic compound, to create an organic dye. The method is identical to making Ferric Chloride, but you use only strong vinegar and steel wool. The acetic acid (vinegar) dissolves the iron and makes iron acetate. If you can get it, 10% glacial acetic acid is great for making iron acetate ... but cleaning white vinegar is just glacial acetic acid diluted to 6%.
IIRC, the same method as ebonizing oak was an old way of making black leather.