The [kind] tag holds values like
MPEG audio file
FLAC audio file
WAV audio file
etc
When re-organizing folders you can do something like:
$If(<Kind>="MPEG audio file",,\Flac)\<Genre>\$Sort(<Artist>)\<Year> _ <Album>$If(<Kind>="MPEG audio file",," ("$Left(<Kind>,4)")")\<Track#> - <Artist> - <Title>
So here you'd get anything that isn't mp3 going into a separate folder called 'Flac' and the first 4 chars (ie 'Flac') of a non-MP3 file getting appended to the name of the folder the album is in.
You can use the [kind] tags in filters to easily just play all your Flac files. Not sure if this is what you mean by 'tag separation' but it may help put you on the path to what you are looking for...