Don't worry about the molera, just be very careful about dropping her since even minor head trauma can cause major damage for these little ones. For some reason, apple heads seem to be more prone to large moleras than deer heads possibly due to the way the growth plate develops as they age (extends further along the axis on a deer head). It's not a birth defect, it's part of a chi's genetic make-up, and while it can pose a greater risk in terms of head trauma or hydroencephalopathy, etc... if you are diligent and know about the problem, you won't have any unexpected problems =)
I've got a soft spot too, but it's a little lower, and it's really soft for chihuahuas!