timos, there are a couple of options available to the check in staff.
1. Upgrade commercial pax into J class, person with higher onload category in Y gets on.
2. Onload staff passenger who can take advantage of upgrade category. So if you have a J upgradeable and they don't then you get on in this case.
In your exact example, the person with the higher onload gets on board first. They'd also get the upgrade because you're not on board the aircraft and so they're not competing with anyone for the seat. They unload everyone they can first and THEN they look at the upgrade. The staff travel website actually goes through this example I think.
If option 2 above is in play, it depends on the day, on the check in staff member, whether there are commercial pax suitable for upgrade, etc. The only thing I can tell you for sure is that the onload category trumps all else. After that is done we start squabbling over who gets moved closer to the front.