This is sore topic for myself and a few others.
The behavior changed a few years ago.
Keep in mind regarding user folders:
The change is that now when you open Cubase, Media bay does an automatic scan of every user folder. With the automatic scan, it will also by default check any box that you have purposely left unchecked. The result is more mouse-clicking and taking time to navigate and filter out things that should have already been filtered out, had there been no auto scan.
Or another way to explain it is when you open a preset, and the tree is open, you have to uncheck multiple boxes, just to see what presets apply to any given project.
They know about this. They say it’s by design, but I can’t think of any logical explanation other than it sort of “dumbs down” media bay for inexperienced users. Personally, when I want something left unchecked, there is a good reason for that.