In my (vaguely similar) system this isn’t a problem. My top level folders (“groups” 
) use relatively immutable categories for my fields of interest (I crossed checked it with the Dewey list to make sure I was choosing top level and not just what I felt was top level, so “earth sciences” instead of “geology”). I have subfolders inside them that are more defined, so eg I’d have:
- Earth Sciences
10.01. Geology
10.02. Climate science
10.03. Ecology
10.04. Specific niche interest 1
10.05. Specific niche interest 2
Etc. If something fits in more than one subfolder (fairly common in earth sciences!), I just put it in the top folder and not one of the subfolders. So if something is both geology and climate science, it might just end up in the “10. Earth Sciences” folder rather than being subcategorised. Hopefully that makes sense.
I don’t file my bills in DT, but I guess if I was doing similar for that I’d have:
- Bills
20.01. House
20.02. Car
20.03. Tech
Or whatever, and all the misc ones would just go in “20. Bills”.
Edited as I realised an error with my numbering.