On SkyView, if you put the transponder in ALT mode manually, you are disabling the auto air/ground mode, which means it will stay in ALT when you land. We recommend you just leave it in AUTO all the time unless specifically directed by ATC to turn off the transponder, or if you are flying formation and only one ship should have a transponder on. Thus, the checklist should not change the mode for you, actually taking off should, just like it does today.
There is a huge certification difference for auto air/ground for a Mode C vs. Mode S for some reason. You are specifically disallowed from using just GPS speed to switch modes on a Mode S.