Tampermonkey can change what's on the web page, but extensions can do much more than that, e.g. add toolbar menus and items to the context menu, add keyboard shortcuts, manage bookmarks, and so on. (See the API guide for an overview [1])
It's true that many extensions could "just be" Tampermonkey scripts. I'd guess they ship as standalone extensions due to a combination of: less friction to install, more discoverable, can extend with fancier features later on, and probably just inertia/ignorance from developers unaware of Tampermonkey.