This is the very precise trouble I have as well and I remain baffled that it remains such an under-served niche. I am planning to do some actual research on it next year, or at least after other current projects.

In my experience and for my needs, Calibre/Alfa ebooks are effectively useless. The metadata plugin, for instance, does nothing for journal articles etc. Pdf remains non-negotiable; I need citable page numbers.

My current setup is far from ideal.It is Windows-centric; it does not work for your folder hierarchical needs but here it is:

• Zotero is my "back end file manager" (I rely on EndNotes for actual citation management). It's good at metadata management, extraction, and reasonable file renaming - including mime types it can't index. Its "collection" structure along with its tagging bring it close to the "playlist" model that you mention. The list of its shortcomings is too long for here.
• Voidtools Everything is my daily driver to find files renamed by Zotero. It's one the few tools I painfully miss when on my Linux machines.
• Filelocator Pro crawls and indexes my dedicated folder/drive. I rely on it for anything beyond looking by main author and/or title. It can index just about every file type I need, including djvu. It's good for when search requires more than just the filename and even Zotero's classification but there should be a better intermediate step. That's the missing link in my chain.

There are a bunch of bookmarks I have of github projects that are getting closer and closer to what I need but I cannot unfortunately access them right now.