I keep them in separate folders and disambiguate using the release group disambiguation and the medium description. Taking the “Paranoid” 2009 UK release, this would give me these folders:
Black Sabbath/
Black Sabbath - Paranoid (2009 album, GB)/
CD 1: Original Album 1970/
CD 2: Bonus Tracks/
I use the same logic for box sets, like Klaus Schulze’s Ultimate Edition, a 50-CD box set!
I may use unorthodox scripting and filenaming scripts, but if you’re interested, let me know.
See also: How does Picard handle saving album releases of different countries?
Find the full script here: Repository for neat file name string patterns and tagger script snippets