The simplest reason that Nexus is 'bad' is that it throttles free user downloads, so you may spend hours downloading a large mod at 2MB/s. There's nothing wrong with a site like Nexus, but Nexus specifically is very annoying to use.
The argument that a mod can only be downloaded from Nexus is a courtesy and not anything the mod authors can enforce. Likewise, you can just download the zip from GitHub and build. There’s no real control the authors can do to make sure their mod is downloaded from nexus. Hosting it anywhere else may be against the mod authors wishes but it won’t stop people from hosting the installer/archive.