cdc, Your BMG version is a different version than the store-bought version. But it's not different or inferior because it's a BMG edition. It's different because the CD title "Chronicles" has earlier mastering of the material than the current CD of the album "2112".
In other words, if you bought "Chronicles" in a store today, it would also sound comparatively worse than the "2112". When Mercury Records remastered the individual album CDs I do not think that they did the same for the Chronicles set. This is probably because they were issuing two new compilation sets at the time, Retrospective. Or if they did, then you may have an older copy (that's why I asked when you got the BMG disc).
By mastering, people here mean the process of prepping a recording for CD format. Sometimes the record labels put a new date to indicate the remastering date (e.g., "(c) 1976, 2002"), but sometimes they do not (e.g., "(c) 1976" only). I think this depends on whether the label feels that a newly mastered recording warrants copyright registration as a "new" work. Obviously, that Rush album was not mastered (for CD) in 1976.
In most cases, record companies will change the artwork or place a sticker on the plastic to advertise a "new mastering". But this is not always the case: the Bruce Springsteen catalogue was redone with no change to the packaging. The Who's Who's Next CD used to be like that too; in the U.S. MCA originally issued a "Steve Hoffman" master of that album on CD, then changed to another master without changing the packaging. (The Who's Next CD is currently a totally different package, with bonus tracks and yet another remastering.)
So with something like Springsteen's catalogue someone could potentially have two similar looking versions of the disc and think, "BMG's CDs are better sounding than my Tower Records copy!"