Please correct me if I'm wrong, but you seem to still be "stuck" on the "old" generation of hardware/technology. If any "inconsistencies" between ORAS and the "pioneer games" occur, then I believe that they can be remedied through direct contact with the "updated game" - in this case ORAS.
First off, as I've already
said earlier in this thread, patches/bug fixes/what have you have already
been done before. There was no WiFi back then, as you know, and this was still accomplished in not just one, but many ways - you could still "fix" your RS today, given you have access to the "fix."
The DS may have been a step up, but is nothing to what the 3DS is capable of. GF had no way of updating the games due to the constraints at the time, and were not about to spend unnecessary resources to remedy a few forme changes between DP and Platinum.
I'll repeat myself,
I am NOT a technical engineer or programmer - I'm not even all that great with computers. I don't know what exactly is and is not possible with this generation's hardware/software. I am merely (lightly) basing this off the fact that we can, and have, receive
updates/bug fixes/what have you.
If it is at all possible, then I believe GF would "force" an update on XY from ORAS to patch any irregularities. The situation could be something along the lines of:
Communication between "pioneer game" and "updated game" established.
"Updated game" sends a message to "pioneer game" to accept this new packet of information.
A prompt appears on the "pioneer game's" screen to either accept or decline the new data.
If "yes" is selected, then "pioneer game" will download and install the new data (perhaps asking to save the game first), communication may be interrupted or terminated so that the game may fully integrate the new data - maybe even a restart to Title screen
If "no" is selected, then communication terminates and the attempted trade/battle never starts.
Of course, this is just how I see the situation.