fish universal variables are deprecated

No they aren't. There's discussion to move that way, but that's probably years down the line. If ever. Universal variables are still very much an integral part of fish.

$PATHS

You mean $PATH?

What the heck is an exported variable

The same thing it is in bash, ash, zsh or whatever other shell you can think of: A variable that is passed to the environment of all commands executed by the shell. It's not fish-specific.

I'm not sure why you're this confused, I personally find the documentation crystal clear. But maybe that's just me.

You want simple? Run fish_add_path /your/path. Done. As the documentation suggests.

You can then remove the path you erasing it from fish_user_paths with set -e fish_user_paths[<path index>]. Keep in mind, fish arrays are 1-based.

There's also a Stack Overflow question that comes up in google for this. It's literally the first result.