No, it doesn't. Acceleration is the same thing as gravity (see Einstein if you want to really get into it). Therefore, if you are braking, you impart an acceleration opposite your direction of travel (towards the back). This shifts your effective center of gravity forward, EXACTLY as if you shifted your weight forward.

When you brake hard enough that your effective center of gravity moves in front of the contact point of the front wheel on the ground, you flip over frontwards.

Your effective center of gravity is the REASON that you do an endo in the first place. Do you not believe that it's possible to endo if you don't shift your weight on the bike? Go ahead and try it, but wear a helmet.