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Most are not.
It is not advised to mix Bethesda mods with mods from the internet. The ingame modding system prioritises mods from the ingame modding system, meaning the load order is guaranteed to be wrong with a mixed load order.
I would advise you to use Nexus Mods, and follow a guide like Vlad's guides to modding Skyrim (you can find them in the guides section)
The In-Game mod menu only lists mods hosted by Bethesda's servers. It won't host other mods that require more than just "install".
"AFT" being one of those that's reliant on more than just the base game.
This same goes for things that rely on the Script Extender (which is an external tool) and will never be hosted by Bethesda. That means anything that uses it (which is a lot of mods) won't ever be on the In-Game Mod section, because they wouldn't work there.
You can, with the Vortex Mod Manager, as it has an extension for it. I've not used the option myself though, so i have no idea how well it works, or if it works.
You can however, download them from the in-game menu, Copy the files to another location, and then delete them from the in-game menu again.
You would then add the files to Vortex, and have it handle everything.
Having both of them working together is a bit questionable. There is that extension available for Vortex ofcourse but as i said, i have no idea how well it works....