How do I configure calendar " leave in X minutes" notifications to use non-driving travel times?
Well, I think you are talking about the Google Now notification, right?

If so, you have to change the option on the Google Now app, not on the Calendar app. 

To do so, you go to Google Now(tap the search bar on the top of your home page) then you'll see the card that estimates your arrival time to your destination, you can see like three vertical dots, tap there and hit Settings, now you set Transportation Mode to Public Transit. 

From now on, the card will notify automatically the time you need to arrive by public transportation.