Well since so far no one has suggested any solutions (and I'm not aware of an alternative to Lidarr that suits my needs) but I also have noticed a similar problem. Many albums download fine, but there's times where the whole artist downloads each 01 01 01 track and it gets complicated.
I believe outside of manually doing it we'd be looking for filebot, but that's paid, or possibly some sorting tools available through foobar2000 plugins - I'm not sure if it exists here but many others must.