It's just Apple struggling between app-centered or file-centered. App centered is simpler and more intuitive to most users, but results in a lot of data isolation. Apple needs to implement some form of back-end data management so that apps are accessing a shared repository of data - even if the user can't directly interact with it like the Finder. As for a file system in general, I still want on for certain things. I keep my LR library organized in folders, my documents are organized in folders, etc.
I'm okay with Procreate files in Procreate, or Photos in Photos. But for my classes, I don't want my PDFs in PDF Expert, my PPs in Power Point, my Word documents in Word, etc. I want them all within one folder titled "Advanced Corporate Taxation" or something like that.
It depends on context and I wish Apple gave us more control over that. Sorry this reply is so long.
I've been using Apple's 'cloud' service offerings since iTools. I also want iCloud to be the solution, but realistically, Apple is not the best when it comes to cloud services and our only hope may be using third party apps such as DropBox, but that depends on whether the app gives us this option. The same with iCloud integration. Microsoft apps seem to allow you to save to several third party services, but not iCloud. In the end, I'm hoping that tagging files and multiple selection is expanded. Search for the name, "Advanced Corporate Taxation" and all the associate files are presented, regardless of the app. Select them all and upload to the service of your choice. Yes, you still have duplication issues, but it would be a nice step in right direction.