That is exactly the problem. And it was not like this in C6. At some point someone decided that C/user folders should always be checked no matter what. And that has ruined any possibility of organizing VST presets.
One moderator says it was “by design” but gave no explanation of course. 
Here is the original post.
The title is “8.5 mediabay still re-scanning my user content at startup!” I may be wrong, but I don’t think there is any problem with mediabay re-scanning the user content at startup. The problem is the re-scan automatically checks folder boxes that the user has deliberately left unchecked. 