That's just how things are, we just run most of the game most of the time. I guess there could be a category where you exclusively run the 5th chamber by using the shortcut, but I doubt anyone would be interested in it since it does not sound fun.

There's plenty of people doing runs of non-leaderboard categories, such as all floors, you can just do it as a personal challenge.

In 1 character runs, we don't use real time, only in-game time. On multi-character runs however, we use real time only and apparently you're supposed to stop it when you shoot yourself with the gun that can kill the past in your last character's run. I might be wrong though.