iTunes sorts such cases in the following way:
Artist Folder
Album Folder
Latter has the files named:
1-01 Trackname.m4a
1-02 Trackname.m4a
...
2-01 Trackname.m4a
2-02 Trackname.m4a
Should Plex be able to understand this and list both CDs under one album entry? It doesn't seem to, when looking at the way it displays such kind of albums.
It seems to be working as expected for mp3 files. So I guess this is a feature request to add identical functionality for m4a files.