iCloud Drive folder structure?

Can someone educate me on Apple's philosophy regarding iCloud Drive folder structures? I want to organise my folders and files by topic, not by software. From the example in the attached image, you can see that I want to have four top-level folders. I don't want the the bottom six folders in the list. (By the way, I do know that Apple uses file pointers, and does not replicate the files within each folder.)

As the number of folders increases, the folder structure gets messier and messier. I currently put "--" at the beginning of the "topic" folder names, so that they sort together. Otherwise it becomes a hunt-and-peck exercise, searching for them among the software folders. Not so bad with a small number of folders, but it gets progressively worse with lots of "topic" folders. I want to consolidate all my cloud-based files (from Dropbox, etc) into iCloud, but I really don't like Apple's folder structure philosophy. It seems like I will end up with a lot of "junk" software folders that are meaningless to me.

Anyway around this? Thx