First, there’s overlap (both list currently installed plugins), which can’t be a good thing.
Second, only Preferences > Addons > Plugins tells you if a plugin is out-of-date, but in order to update it, it’s best to first remove it and then (re)install it (in case the name has been changed; I’ve found that out the hard way…), which requires Plugin Manager.
Wouldn’t it make more sense to put everything in one place? By everything I mean list all available plugins, show which are installed, tell which of those are out-of-date, and allow to install, uninstall and remove plugins.
Also, because of the above mentioned issue, maybe the built-in plugin update process should just include an extra step of removing the old version?
Finally, wouldn’t it be nice if there was a canonical way to manage scripts from within Glyphs, like plugins?