As a rule of thumb, any two albums with different catalogue numbers should be separate entries regardless of content.
And as seanne mentioned, albums with the same catalogue number but drastically different packaging can be given separate entries, especially if scans are available for both. Here's an example (not a good one since they're released on different dates):
KSLA-0027: planetarian Drama CD – a snow globe
KSLA-0027: planetarian Drama CD Box 1 – a snow globe
If the disc contents are identical (would be good to verify this -- it's technically not a "reprint" if the tracks are remastered, etc) then both albums should be linked together, the second one as a reprint.
If both albums are released on the same day, the non-limited release takes precedence. As for "alternate versions", example below:
SW-006SF: eternal feather - THE MAIN THEME SONG OF "ef - a fairy tale of the two."
SW-006SM: eternal feather - THE MAIN THEME SONG OF "ef - a fairy tale of the two."
The earlier catalogue number (F < M) takes precedence.
Right now we don't actually treat
discs as an entity in our database structure, otherwise we could point both albums to the same disc ID and your concern would be pretty much solved. It's definitely in our future plans though.