Keep in mind that For Glory is simply a "quickmatch" mode. If it was just named that, we wouldn't be having this conversation at all.Sakurai lumps custom moves and equipment under the same bucket, so you can't deduce custom moves are unbalanced from that statement. Either way it's not like he's a good judge of 1v1 balance, what with the only stage being Final Destination. In practice custom specials aren't broken.
Often times "balance" is mistranslated in statements like this. Sakurai routinely talks about the "balance" of the overall gameplay experience, reaching far beyond the character balance that everyone here is singularly obsessed with.
Custom moves being disallowed in quick match is imo a bad call, but understandable since it is an unfair, unbalanced experience for newer players who may not have some of the custom moves and simply want to play a quick, fair game.
A tournament or games with friends are completely different. Sakurai accordingly said, "please use custom moves with friends" immediately after the previous much-quoted statement.