What's the difference between general PC game modding, Bethesda modding, and cheating?
General PC modding
This is modding that can be done in basically every PC game ever. Most of the time, you'll need a 3rd party program to set it up or running in the background in some other cases, modifying the game's executable file. There's very limited use of this kind of modding, people mostly mod their games this way, whether to improve the visuals with Reshade/ENB, autohotkey, Widescreen fix, or cheat with Cheat Engine, trainer, or some other programs. Some games running in certain engines also enable you to 'mod' the game by modifying the files (usually called .ini tweaks). This is NOT what people mean by modding when talking about Bethesda games.
Bethesda modding
Now, this is the real deal. When people say 'modding Bethesda games', they're referring to this. This is generally exclusive to Bethesda games because of their unique engine and modding tools from Bethesda (Creation Kit) and other tools created by the community. Most of the time, this kind of modding doesn't require you to inject something (except script extenders). All you need is to download the mod files and put them in your game's folder, and that's it. The more convenient way is to install them using Mod Manager. Most mods fall into this category, including the most popular ones such as Unofficial Patch, adding/modifying textures (character, weapon, armor, environment), special effects, animation, and more.
So basically, modding is indeed cheating because it can give you various advantages depending on the mods you choose to install. However, past Bethesda games are offline, so there's no problem there. In this Fallout 76 case, the email regarding the ban specifically says "The account was detected to be running a third-party application" which means that the user is being accused of using the first kind of modding. In online games like this, there's usually an anti cheating system which automatically detects any 3rd party program running in the background. In most cases, the anti cheat system would detect any 3rd party program as a cheating tool, so yes, including reshade and autohotkey.