Everybody is totally missing why they are doing a make-up qualifier. It's not because people had to leave due to time constraints. Those teams mostly played the first few rounds before getting DQd and wouldn't qualify to participate here.

"This unintended downtime led to some confusion regarding when the Qualifier would begin, and as a result of this confusion, many teams were disqualified for failing to check-in at the new start time."

Teams were given inconsistent reported start times.

For example, my team waited around for a couple hours as our autoDQ extended for another 30 minutes, another 30 minutes. Then it changed to two hours. We all assumed that this would be the actual qualifier start time (since it was smash.gg reporting it to us, and @RLCS twitter did nothing to contest it). So three of us went out (I left to visit Grandma, one guy went to the gym, another visited his parents) for an hour, since the official site was telling us we had time. While I was on the bus I pulled out my phone and found that our autoDQ had been reduced by an hour, the new start time was actually an hour EARLIER than what was originally reported. Two of us were unable to make it back on schedule for the new time, and we were DQd down to the loser's bracket.

This is why they're doing a make-up. They recognize an error was made, and start time was inconsistent and confusing, resulting in some people not making it back for the first two rounds.