Some folks like 1+ inches between the top tube and the "stuff", others ride such that they can't stand over the top tube without leaning. It's all a matter of preference. Aside from ym modern Cannondale all my top tubes nestle quite snugly "up there".

As long as the bike fits you and is comfortable I wouldn't worry about the standover. You just lean a little bit so you don't crunch the top tube. However, if the way it is not makes you feel unsafe then I would look at doing something different. Coming to a stop and starting again in traffic is the very last place you want to feel the slightest bit twitchy or tentative on the bike.