Yeah, I agree using file extension is too general in many cases, especially yours.

What you describe sounds like something I've referred to as "selectors" before - define selectors to apply a ruleset to. Selectors may include location, bit rate, genre, file format, anything!

What I also meant is to be able to set different cataloging rules towards these libraries.
so:
Low q flac:
- album art 100x100
- Naming convention
- tagging
- etc.

HQ flac library:
- album art 500x500
- Naming convention different
- tagging - different
- etc.

But just having different source and destination dirs for lq and hq would be enough.
Just to process all the files from these 2 directories without mixing them in the end.

File extension is very vague category. As i have flac files which are 24/192hz and i do have ones which are 16/44.1. Some are stereo and some are 4.0 or even 5.1 channel.

Currently i keep my standard quality flac files in one directory, and in the second directory i hold my HQ/HD albums, 1 album may be 2.5gb in size.

I would like to keep these libraries separate. To not mix HQ with normal flacs.

I hope that makes sense.

So you want to use the file organisation rule to organize by bit rate, sample rate or something else? What exactly is the differentiator?

This only works in some cases but https://www.blisshq.com/music-library-management-blog/2011/05/20/organize-music-file-extension/