You can’t change the default set but you can create your own ones and then not use the defaults.
Open the Plugin Manager and click on the + symbol near the top right. You then get the option of creating an empty collection, adding all the plugins or copying another existing collection. Then you name your new collection and can then start moving things around and/or create your own sub-folders.
Much better than the default bizarre collections as you say. I think this came in with Cubase 8.