An explanation of the balloon in flask demo (inside out balloon demo) 

Yes! It is an ongoing misconception among both students and teachers that the size of a balloon is dictated by the point at which the inside and outside pressure is equal. However they are never equal due to, as you say, the mechanical (potential) energy stored in the latex molecules, which only increases as the latex molecules stretch (balloon gets bigger), which means the inside pressure is always greater than the outside pressure. This is why we hear a pop when the balloon bursts. If Pin = Pout, there would be very little sound when it breaks, but as the balloon gets bigger, then Pin >> Pout, and so the break results in a large rush of gas from the balloon creating the pressure wave we hear as the pop.