I like that your main argument against trees for organizing files is that people use specific applications per file type to organize them... _in trees._ Photos are sorted by year first and album then. Songs are sorted by artist first and album then. People understand trees just fine.

Also, the problem of being unable to put the same thing in more than a place is a) not one fixed by app silos b) part of our daily life while sorting physical objects c) fixed with filesystem links (soft/hard).

Your argument only proves today's mainstream file management programs/save as dialogues/etc. are inadequate. Trees remain the best simplest model to organize files in a filesystem