fwiw, there are more examples arguing for the current ruling, which were provided to both team fire and WMs.
IMO, if this was caught shortly after the deadline before the match started, then editing the deck for a penalty is acceptable. Because the match had already started, I don't think that it is acceptable to be able to edit the deck (again this is my opinion based on my experience as a WM). What if I brought a deck against an opponent that used nightmare, I could easily play game 1 and say "oh shoot, we forgot to change our mark to whatever element because we were expecting nightmares".
The current rules are vague in these situations, and a ruling either way is not wrong. Different WMs will rule differently based on different reasons. I asked the WMs to clarify the rules regarding these situations for future rounds/wars, but as always it should be consistent with the ruling that was made. And a WM next war can change these rules that would go in the opposite direction if they want.
Lastly, if the roles were switched and it was me or aether that made this mistake, I'm sure there would be a lot less "drama" with this ruling.