Stupid Format Wars (or, How to Best Organize My Data)

I have been reading here a while, and I am now getting serious about a "real" server, as the fan on the Mac Mini is killing me.  All of my top choices use Roon, and I now have a license and I am starting to use it.  This has motivated me to speed up my project of re-ripping all of my CDs.  However, the more I think about it, the more elaborate the ultimate organization of my data becomes, so I thought I would ask here and see if I get any feedback . . .  Requirements, as follows:

* Some of my files are for items for which I have a canonical source, and some are not (think bootleg sets) or the MP3 file is the canonical source (think podcast episodes).
* For the items for which I can choose what it's ultimate format is, I need to support Apple and non-Apple ecosystems.
* Both iTunes and Roon support WAV, but neither handle the (lack of) associated metadata well.

As such, I think the simplest organizational scheme fundamentally consists of three directories, as follows:

* "FLAC" and "M4A": Two directories for which I have the canonical source, the content is mirrored, and which contain files of the associated format, _with_ included metadata.
* "MP3": For items for which I don't have the canonical source, or for which the canonical source _is_ the MP3 file.

Then, I would be able to point iTunes at "M4A+MP3", and point Roon (and, more importantly, other, non-M4A supporting ecosystems) at "FLAC+MP3".

IAH, this seems way too fucking complicated, but, given the requirements, I don't see anything easier.  Anyone out there have any thoughts?