Having ridden our upright only 15 miles, our experience is limited to the recumbent on which we can coast more slowly (3 mph or less) than on the upright (4-5 mph) probably due in part to a lower center of gravity. Other than this coast speed factor, I would expect our technique on the upright to be about the same as on the recumbent. As to your two scenarios, as we approach a stop I will advise Cyndi, "stopping" at which time she will unclip but keep her shoe on the pedal. I will remain clipped until I'm certain we will come to a dead stop or if not certain we can no longer coast without falling. At that point I'll unclip and both of us will put our left foot on the ground. Once our feet are down, regardless of what happens ( the light unexpectedly turns green, motorists yelling at us etc.) we must restart utilizing our normal technique. If she is unclipped and I'm still in and the light unexpectedly turns green, I'll thrust and she will reclip.
Other than one ride when we were learning how to ride the recumbent (and didn't know any better) we never have one of us clipped and the other with a foot on the ground. I remember that ride well. The Vision owner's manual suggested the technique with the stoker ( Cyndi, 140 lbs.) balancing the bike while the captain (me, 165 lbs.) remained clipped. (By the way, I'm no longer the captain or pilot, I'm the helmsman) After 15-20 miles and 10-15 stops, my stoker pointedly advised her blissfully ignorant captain that she could no longer balance the bike. It was too heavy. I advised we would switch and I would balance and she would stay clipped. Well, after about two stops, I thought the heck with this and I pulled into a parking lot. For the next 1/2 hour we tried different techniques finally settling on the one we use now. We are most comfortable with this method so this is the one we will practice and use with the upright.