Plex should actually be able to pull the relevant information from Flac.
As you have already checked Advanced > Prefer local metadata the only thing coming to mind is that Plex does not automatically apply that to existing records.
There’s 2 scenarios to get this to work:
- easy way: refresh metadata for your library
- if #1 doesn’t work you might need to re-scan the files; for this to work, you’ll first need to make Plex forget it already knows the files (and has them incorrectly matched). To achieve that, you’ll need to perform a “Plex Dance” → remove the files from the folder monitored by Plex, scan the library for updates, empty trash / clear caches, return the files to their supposed location, scan for updates again
Definitely give #1 a try first 
Edit:
You can define some additional path for Plex to look for related music videos. (if you have music videos that are not stored inside your regular music folder organization).
From https://support.plex.tv/articles/205568377-adding-local-artist-and-music-videos/
In the Local music video path field, specify the full filesystem path to the location of where your music videos are stored
