I don't really understand why they are used instead of just refering to whatever they are aliases for directly. Can someone give a hopefully simple explaination?

You can place scripts, packages and spells on them, that are only applied while the alias is applied, the same happens with the very reference to their own, you can use a lot of checks and operations on aliases that will be applied to different NPCs when that alieas is applied.

Then, you can use various of them to apply their uses with different priorities (depending on the priority of their own quest). Their usefulness it's eaisers understanded unce you start using them.

Attaching scripts to an object, adding packages to a package stack, adding spells etc directly to an object in the editor is a pain.

With aliases you can add them to the alias and then fill the alias with an object in multiple ways (get the object from event data, find a reference in the loaded area, choose a specific reference in the editor) and if you want to remove all those scripts, packages, etc from the object all you have to do is either clear the alias or stop the quest.

Two big problems with adding things directly to references.
1. If other mods edit that object at all, the first loaded mod will lose all changes, scripts, etc.
2. After you uninstall the mod scripts added directly to an object will hang around in the save and cause problems.

Aliases stop both of these problems, plus they're convenient.