The item gets some NBT data tacked on to it to change its name and ensure the game knows to change it back properly.
Since you get the actual item, you can use it for crafting but you probably shouldn't, as you'll lose all other attached items.
To morph the tome into another mod's documentation book that is added to it, simply right click and pick the one you want.
Shift-right clicking a block from a mod that has a book added to the tome will morph the tome into that book. If you have multiple from the same mod, it'll take the first added.
To unmorph back into the tome, left click the air.
While in the standard "Akashic Tome" item, you can right click a block that does not have a documentation book to be taken to its wiki (this uses the Botania Wiki API, and will default to the FTB wiki)
To remove items attached to it, drop the item using Q while shifting and it's morphed into the item you want to remove.