You're confusing punishing with challenging. If the floor saves started later, how would that change the strength or number of mobs? Allowing later starts with no pomanders would make it more difficult, not less. The reason for having to start over is content padding.
OP is asking for a QoL change. Should SE revert the hundreds if not thousands of meaningful QoL updates the game has received because things were one way at one time?
Did what in A6S? The overall length of the floor was about the same as any other duty. If you wipe 9 minutes into a 10 minute EX or normal trial, you have to start from scratch just the same.
There were two complaints about UCoB: Nael's lines and the fight being a bit lengthy. Ultima was made a few minutes shorter as a result.
From some of the comments, you'd think it was a common thing to leave the instance and start over if you wiped on Neo or Godka. Like anyone looking to do higher floors would decline the option to start higher than 21 if the choice was given.
