There are only
- Old game
- Special Edition.

Anniversary Edition is available DLC. If you buy it, DLC allows you to download and install all previously released creations for Skyrim SE. It is nothing more and does not change the game version. You would only need that, if some mod specifically needs to hook up with some of the creation content. Installing such mod would be your own choice to begin with and dependency would probably be made for ingame collectable items.

Otherwise the user hassle with game versions is 100% self-made problem. It was not done by BGS, but modding community, which managed managed to make it even further complex by branding post-compiler upgrade version of the game as "Anniversary Edition" (or AE.)

There is no Anniversary Edition of the game. If you have up to date version of Skyrim Special Edition, then that is already version "AE" for all counts. If you experience any confusion about which file to use, just check the version number.

So, is the 2016 SE edition worth it if I already own the base game?

Personally I would say yes. I haven't been looking back at Oldrim from SE.

Special Edition has 64bit architecture, superior memory management, fixes and patches LE never got and very active modding community. SE can run mods and tools that would be impossible to use with LE.

Few things to note:

BGS on occasion posts creation updates, which will change executable version number. It is smart to backup exe and/or use few other methods to delay effective update, or mods relying on Script Extender will not work before xSE update. They DO announce these updates in time, so we know either to take precaution or break.

xSE and AddressLibrary are usually very quick to update though.

BGS added few free creations with the game.

• Rare Curious ads new crating components and trade items in to game. That's nice.
  
  
• Survival mode is now inbuilt mode in the game. This mode can be toggled on or off from menu, so it doesn't make pointless changes either.
  
  
• Fishing ads fishing mechanism, gear and quests in to game. You can complete those for your leisure, or just completely ignore the whole thing.
  
  
• Saints and Seducers can be a bit more troublesome. That one includes two opposing factions in to game, but they mostly all act like bandit bands. They are fare more powerful than usual bandits, so it is wise to avoid them early on. They do not really patrol around though, so matter of avoiding them is to spot and avoid their camps. I was against adding this one in to base game. It didn't fit the theme of other addons, which were mostly optional features that you could just ignore entirely, or choose to have fun with.