Why would higher fork contribute significantly to breaking the frame?
how does a higher fork contribute to higher stress in the frame?


By creating a longer lever, and stretching the end of that lever to a greater angle, it transmits more force to the bottom of the head tube (the part of the frame where the steer tube passes through). This can cause damage to the head tube itself or where it joins both the down tube and top tube. How does this happen? That longer lever is essentially trying to pry the head tube off of that joint.


  What is the effect of lower fork than the original?


A fork with less travel (or similar travel but a shorter overall length) will steepen the head angle which will make your steering a bit quicker and more responsive. Now, this does reduce the force applied to the lower part of the head tube, but due to the change in angle, increases the force applied to the upper part.


  Does bike A, being sold with higher fork than bike B, mean that A's frame is stronger? Or is it just different geometry?


Simply: no. Frames are like any other product where the visual inspection does not guarantee that the assumption is true. For instance, most tapered head tubes with fork travel X are probably stronger than a straight head tube with the same fork travel. The purpose of the bike will also determine a relative frame strength. A dirt jump bike with a 100mm fork will handle way more stress than a XC frame with 100mm fork. The trade off is usually flex, weight, or another metric.