Love my IJ. On the flipper alignment question, I assume it's designed that way but not sure how. The flipper range is determined by the mechanical parts underneath. It may have something todo with the angle of the in lanes being steeper by a degree or two which would cause the end point of the upward flipper travel to be lower.
Two solutions. Realign flippers to angle slightly higher at rest or file down the plunger to allow for more travel. Not sure how that might affect flipper performance