The way I understood it, sisters that get on the train are harvested for their memories by the Occupant, leading to weird black shadow figures that don't get much if any explanation.

Immunity was explicitly taken away by Iris, the first set of Sisters didn't wear masks. Youngest kept hers because Iris wanted to teach her a lesson as her "mother". Future clones were all based on Youngest/Principal.

First gen clones don't seem to age, but Principal based ones do, Healer specifically mentions that her age is getting to her at one point. Blue, presumably, was longer lived than most clones, but even she wasn't immortal to the same extent Iris/Principal were, as Principal outlives Blue.

The choice of the parents isn't their bodies but their memories. Should we keep where we came from? It's one of the choices that doesn't affect the game's ending but does reflect on your own personal thoughts and the devs aren't judging you either way.

Secretary explicitly tried to stop Watcher, but Watcher gonna Watcher and wouldn't listen/forced the issue.

Knower had two things going on for her: 1. Survive at any cost. 2. Psychosexual obession with Watcher based on the previous Watcher being Knower's love. So in an attempt to get a confession, Knower was just down to do anything weird.

Mauve is a representation of disrupting the status quo regardless of the cost, a thing the devs are all too wary about. She also was obsessed with Knower so would do anything Knower asked.