The wording of the TT rule to me sounds like a 1 day round for singles where the player who didn't send had 0 chance of winning so its basically a bye anyway.
To me it wouldn't make any sense to have 1 alt team and by placing this alt team correctly you're demoing 2 teams from the draw and placing a bye there.
As for which team gets replaced, IMO the higher ranked team should remain in the draw as all the other rules seem to want to reward the higher ranked team.
I'm part of the team that was replaced by this, but I agree that should be in this way the higher ranked team have to stay in the draw, I think that is something that have to be clear in the rules of TT and DTT.
The only thing that I think that it will better is that team that get replaced, have to be the worst ranked betwen all that didn't send not only in the match that two players didn't send. I think that any case it will be us with catgamer.