I'm really not liking the new system either. I haven't been killed while logged out yet, but it's a pain in the ass if I'm in a dangerous town and I'm not even safe going to the WM for a minute. Like others have said, it's kinda stupid that I need to log out if I'm traveling and get a phone call or something.
Also, I have been getting random encounters while idling over towns, although I'm fairly sure that's nothing new. IMO, if the new system stays is place then I feel like you should be safe while hovering on a "civilized" tile (like the green spot for NCR, Hub, San Fran etc.).