As others have mentioned, the 7DTD Mod Launcher will help resolve your issue with running multiple versions.
As for the future of the game, my hope is that TFP will build in a mod manager right into the game once it goes gold. I've actually been playing a lot of Farming Simulator 22 lately (leave me alone, I'm an old man) and they have a manager built right into the game and it works (almost) flawlessly. Not only can I browse and install most mods directly within the game, but I can also choose which mods I want to be enabled on a per-save basis.
Given TFP attitude towards mods (they're very much in favor of them) I think it would only make sense they do something like this in the future.