(I believe that) Autoclosing a revision when the commit(s) associated with it appear on a branch other that the master is not expected behavior.
Specifically submitting a diff and then pushing your local branch to the server will close that diff.

It's not really obvious what is happening either, because the diff is closed with a message like:

Closed by commit rXXXXXX

and you have to open the commit URL and realize that it refers to the branch that you just pushed.

I've gone through 4 waves of people in our setup doing this and the default behavior always perplexed them.

Since this is an option that is not shown during the initial wizard for the repository creation and it's not expected behavior, I don't think people will remember to change the setting on every repository that is created even if I note it somewhere.

A global default setting, that can be overwritten by the repository would be helpful in order to enforce this.

I can see that this has been brought up before (T5630) 3 years ago, but I thought it needs readdressing.