There has to be a better way than getting a free bye if your opponent is inactive or if you don't have an opponent. Being able to mod your deck anyway you want without an opponent to stop you is an absolute godsend in a game like this, putting aside the fact that you are 1/6th of the way done. The most I can think of at 2am is some sort of "Designated dueler" who will duel them with their opponent's mark and attempt to make a change from that mark to a random mark (Chosen by an RNG generator). Again, not a great idea, but I think its better than giving away such an advantage.
There's also the issue of when people who are more active than their opponent have to make their deck changes. There has to be a day or two between rounds just for those people to post their morphings, or else they get another advantage over people who actually have their matches (morphing after knowing your opponent's element and deck).