If your connection is Schengen to non-Schengen, as it appears, you would be registering before going through passport control. Reports are that the registration takes effect immediately (I haven't tested this), so you would be able to use the Easypass lanes right away, which might offset the 10-15 minutes needed for the registration if the Bundespolizei office isn't busy. Fill out the application form ahead of time, of course.