If I didn't buy an item brand new (stand-alone or as a bundle) I wouldn't assume anything about how it was released. However certain I feel about my guesses, once I submit something like that with part numbers, UPCs and scans to the DB then it's basically set in stone and future collectors will treat the information I guessed at as gospel.
I do have a few titles lying around that I've left out of the DB for the same reasons listed in your examples, where adding it could potentially hurt the DB more than it helps. Like this one that had a sticker UPC on the back:
[img width=700 height=381]https://www.mediafire.com/convkey/ddd8/1ix7fuyu4dfbe196g.jpg[/img]
And I actually bought that from a legit retailer, only later I figured they
probably repurposed it from some sort of bundle. Anyway, if you're lucky you'll find reliable info on other databases (assuming they didn't just guess themselves), like I did with this game that was supposed to go in a double pack -
http://www.rfgeneration.c...nfo.pl?ID=E-087-S-07250-AI think that as long as a bundle entry in the DB is clear enough about it's contents then there's no need to add any of it separately. Although that may be wishful thinking since it's often hard to get good pics of oversized bundles like this one -
http://www.rfgeneration.c...nfo.pl?ID=E-215-S-01650-A