If those 'similar' decks are what caused this whole thing, then it's kinda ridiculous.
I personally feel save states are fine in some situations (quick exit from the game to restart for example) and in others they're obviously wrong (deck resetting in a race for example).
If it turns out that resetting via save states enables an advantage over consoles in regards to similar decks, then it should probably be looked into.
However, I find it a bit suspect that this issue is brought up after m13 obtained the record, despite this issue being known beforehand.
As for the 'ruling', I agree with it. If save states do create an advantage, it's unfair on the people who run this game on legitimate consoles and copies of the game. I play the game on emulator (at least on NTSC), but if I ran this game on console and saw people gaining an advantage by save states I'd probably just stop.
In regards to m13's run, he worked for his PB and obtained it before this rule was in place. I feel as a community, we should be praising and celebrating people's runs, not illegitimising them. As cyber said, his 'advantage' has not created some record than cannot be beat, it's still perfectly beatable.