They may be designed differently, but they work the same. Maybe a few movies would need to be changed, but for the most part, it's the exact same.
Boobs don't get in the way that much, dude.
Besides, for women who get below a certain body fat percentage-- ie, really athletic women-- the boobs are the first thing to go.

You're totally right that our bodies start from different places. I have to play a lot of catch up with my upper body strength. Some of that is because I'm "naturally weaker", but some of it is because I was being told my whole life that women have no upper body strength, so I never bothered to work on it. So saying that women can't do parkour just perpetuates that kind of thinking. Something to think about.
On the other hand, I have other abilities that give me advantages. I have a dance background, so the technique parts of parkour are easier for me than for dudes who just muscle through it. I have good abs and I'm really flexible, so crunches and other things are no issue for me. Also, being light has real advantages when you're holding yourself up, and I'm lighter than almost every guy I know.
EVERYONE is different, and we all have to approach parkour from different angles because of it. To draw an arbitrary line between genders just means we aren't being creative enough when we think about how a certain set of abilities should go at it.