John, I'm a new-comer to PDR13 (and have never used earlier versions) but I really like this behavior. Having the video pause when I press the mark in/out (on-screen button OR via the keyboard) allows me to fine-tune my selection, particularly if my reflexes weren't as good as they should have been. I use the [ and ] keyboard shortcut with my right hand and my left is on the spacebar so it's really easy to start/stop.
There is no preference setting for this as far as I can see.