I did indeed play around with the crafting, but maybe either I misunderstood the OP or you misunderstand me
1. Using 'disjoint' on the item will strip off every prefix, suffix and enhancement, but the item itself stay intact. So it keep things like the base-material an guild-slots (and probably even the look, which I indeed haven't tested yet), preparing it for crafting. This if I understand is one of the reasoning of doing this to a named item at all as it should preserve the look of an armor or weapon. This would then most likely as well keep the name as this name neither include the prefix nor the suffix. It is in fact the old item, just the 3 properties are cleaned. Also it would mean to probably keep the damage dice or crit profile, which of named items is sometimes different then from a regular one. To just convert a SoS into a plain simple Greatsword wouldn't gain you anything. The Name is a fixed element of a named item with its own unique loot table entry and therefore if allowed to 'disjoint' will lead to issues.
2. For what purpose if not to keep one of: the name, the damage dice, the crit profile, the look, a special property that can't be stripped like the guild slot? Otherwise it would be just like throwing this weapon away and get from Korthos a masterwork Khopesh. As of right now it looks like that the item really is taken as is and just the prefix and suffix element are removed together with the enhancement. A named item has no prefix or suffix, which would mean to add additional checks if certain properties stay on the item (Guild slot, damage dice, crit profile...) or not and it certainly is a likely place to get an exploitable error at this step. The guild-slot is just an example of a property that is not affected by the disjoint which already tell us that it is somehow attached differently to the item.
3. How you know how the minimum level of a named item is coded to the named items? Maybe it is a property like the guild augment slot that just add a '-2' to the item. You know how the guild-slot is coded on the item? Maybe the suffix and prefix part is coded on a item in a way that you can easily set those to null, but the additional information like augment slots and minimum level is stored somewhere else. As said in (2) doesn't make any sense if you would strip it from everything as it would be cheaper and less troublesome if you just get a masterwork weapon from Korthos. Why then bothering Dev time to implement additional fixes or have the danger to get it exploitable?
It is your assumption that '
in programming terms, you aren't really modifying an item so much as you are generating an entirely new one anyways' and I just say your assumption may be wrong. I don't believe they replace the item with a new one. That would afaik mean that they would have a table where for each weapon a corresponding blank is referenced which would be a total overhead. I indeed believe that the item itself stay the same, but all fields that refer to a enhancement, prefix or suffix get cleaned. A named item has however properties that don't fall in this category but all that property would need to be cleaned as well. Or as you suggest, you would need to add code that make actually a copy of the item but then this copy will probably not keep the look.
4. This is under your assumption that the graphics is just a simple reference and that the Epic Stone of change not for example use this kind of reference to check if an item is Epic or able to made Epic.
I just think it is far more tricky then it sounds like, especially if you look how often properties of new items get mixed up and need quite some work to get them corrected. If they implement this and by accident the crit-profile of a SoS get transfered to a blank then you can be sure the hell will be loose. And for the huge amount of named items you would need to add a ton of additional checks to prevent this.
Don't get me wrong, I would like to have the look of a named item that provide me nothing special transfered to an own crafted item. But I however doubt it is that easy to implement the strip of named items compared to the danger of an exploitable error.