Depends on what you define as 'collector standpoint'
If you're collecting for yourself and personal use (like I do). Doesn't really matter and up to your discretion
If you're collecting to resell later on then serials should at least match all across. As most potential buyers will check especially if the game is uncommon and/or expensive.
By no means am I an expert but as long as all the barcodes, serials, cart/disc codes all match then it **should** be all the same. Most games might have ONE variant: a greatest hits/platinum version or sometimes a variant front cover. Even for the most part a majority of variant case covers share the same serials as the regular edition.
One experience I had was with Radiant Historia on the DS. I bought a brand new sealed regular edition off amazon 3 years back. Then I found the launch edition outer box and soundtrack for $15 one year later loose. I bought it and I compared the serials, box code, game cart serial of what I bought to about 4 different launch editions samples online and to 1 actual launch edition I found at a local retro game store.....I found them all to have the same serials. From that I concluded there was no difference, which makes sense from a manufacturing point. If Atlus made 2 different version than that would be 2 different production costs,runs,registrations and 2 different inventory SKUs to keep track.
Lord of Magna: Maiden Heaven for the 3ds is another one that all serials are all the same. Whether launch edition or if you piece together your own launch edition.
I would only see this as an issue on actual rare/uncommon,expensive games. However, if a game is expensive and rare then it's likely to have a low print run and most likely not have a greatest hits/platinum version or any variants to worry about. Rule of Rose and Kuon don't have Greatest Hits versions if they did then they wouldn't be expensive....so buying it loose and buying a case/manual separate will yield the same serials and disc codes. Not to mention if you're looking to spend at the higher tier then it would be wise to research what you are buying or just pay the premium and buy new and sealed if you can't be bothered.