Within MindNode I can move a file into iCloud Drive. It shows up in the MindNode iCloud folder as in test.mindnode below. Note it has no size.
Within the Finder I can move a file into iCloud Drive. It shows up as in test2.mindnode above. It has a file size.
Both behave the same way on double click. Both show up similarly in MindNode.app on my iPhone.
test2 behaves like a document. I can create an alias of it. test IS an alias, it points to a document at the root of iCloud Drive.