The issue you are up against is the difference between the track (i.e. file's) 'artist' attribute and the directory (i.e. album's) 'artist'. For me the only option that makes sense is to keep these distinct.

You've obviously come across the case where the album should be assigned to 'Various Artists' (or your equivalent value) while each individual song is tagged with the appropriate artist. This is, however, just one example of the issue, look at Ellie Goulding's album "Halcyon", most of the songs (as you would expect) are by Ellie Goulding but one is by Calvin Harris & Ellie Goulding. What to do in this case? If this song is labeled as by Ellie Goulding then searching for material by Calvin Harris will fail, if it is properly labeled it gets shuffled off to a directory on its own? So yes this is exactly why you need to manage your own music files

There are a number of ways to do this. The way I personally do it is to keep the tags completely separate from the files (in a single CSV file in my case). This lets me define any attributes I want, like a "album-artist" and "album-album" attributes in addition to the "song-artist" and "song-album" attributes. Then I can insert a subset of those tags into the audio files via the MP3::Tag and MP3::Info packages.

I find that using a range of Perl scripts to coordinate audio files, directories, the CSV file and MP3 ID3v2 tags ensures my music is exactly where I want it.