I've ridden a bike that may be a size or two tall... for years. And the Family Jewels are still intact.
It just doesn't matter that much, and I find it comfortable to sit on the top tube when I'm resting at a stop light. I'm sure I've survived more than a few emergency stops over the year. I can't remember many, but I did snag my trailer on a plastic guard rail a few months ago. Stopped cold.
Using toe clips, or clipless cleats, most of the time I'm only unclipping one foot anyway. I probably am rarely standing two feet flat on the ground.