To me the reasons that question should be asked carefully are that:
You’re interviewing to join a company that works a certain way and (unless it’s a startup) does so successfully enough to pay a salary. There are many valid ways to do source control, and a lot of people like to moralize their favorite one and make bad assumptions about how a company runs based on whether they use git or Perforce or Subversion.
The important question is just whether the company uses source control, and that’s what the Joel Test this question was borrowed from asks. Asking which one is fine, but requesting justification for it is the part that could come off as naive and/or condescending. That part of the question to me feels somehow a tad aggressive, and it feels focused on details that matter far less than whether the product ships or not.
Given a random interview at any size company, chances are high that the person you ask did not make the source control decision, and does not know why it was chosen. They might want to rationalize or justify something, but in any case, it’s probably not going to change, and it doesn’t really matter why it was chosen.