I would suspect that Nikon does not allow stop-down metering because the amount of light necessary to meter is reduced and the relative amount of the stray light entering from the viewfinder starts to affect the meter.
Set the camera to A mode, put the cap on the lens and switch the direction of the viewfinder ocular between darker and brighter areas. You will see the shutter speed selected by the camera jumping around. That's the sole reason for the eyepiece shutter.
I think the ocular is normally covered reasonably well by the head of the photographer, but the ocular would be covered less optimally if the photographer wears glasses, which should make the stop-down metering more inaccurate.
Obviously the mirrorless cameras are immune to this problem, and thus there's no problem with the stop-down metering.