I also thinks that if a team can create a legal deck, its not eliminated. Sub to avoid 2 duels next round seems valid to me. Offset vs MEGA vaults? C'mon, I would love to be in team aether situation. They have cards to counter almost anything, while we need use a lot of strategy and crazy decks trying not let them counter our decks easily, and so we need some options. But if we lose, we are most probably eliminated. If I remember it well, no team won after having like 40 cards in vault.
About the bye, like I said, I would make it random, or give it to the team in the middle position in standings. When weakest team get it, it can overlast other teams, like time survived Darkness this war, and I dont think its fair.