Besides the standover height, which did you prefer? I imagine you sit a bit more upright on the larger Jamis than on the smaller Giant.
I wouldn't worry too much about touching the top tube. Of course it's not ideal, but you can still stand over it, which is the important thing. The only thing you won't be able to do is move the bike while stopped without getting off of it, but that's awkward with any size bike. It's always better to get off the bike before trying to reposition it.