From the database level, the only thing you need to do for my suggested system is create another relationship in the database where any deck can assign it’s “parent”. Then you either have chains (a tree of some sort; for netrunner players think daemon trees) or everyone points at the same point and you sort them by date order. Designing the UI if you go this way and making sure the whole thing is optimized is the real trick, but that’s not that unusual. Databases are usually pretty simple. The comments thing would require either date & time look ups (if they exist) or a conversion of the data and a new item to track linked version to say everything that exists is currently on version one of a deck, and then the increment can happen naturally as comments happen. The link is probably more robust, but it teathers you a bit more by binding items together in ways they weren’t before.
I think the real question is: is this usable? Alsciende has been a better judge of usability when implementing his website than I ever was in my short web endevours of yesteryear. So, I’d trust him to pick a good option when presented with most concerns. It’s probably more useful to him to hear what our use cases are. Things we want to be able to do. Rather than ways he could fix it or features he could implement.