Just for info, it seems we have not only 2 configuration screen but 3 different configuration screen (maybe 4). TN+TN, IPS+TN but also IPS+IPS.
Yes some rare consoles have also an IPS touchscreen with the combination of the IPS upper screen.
I confirm with my case. Today I just checked and compared my two N3DS XL.
Result is I have one AUS N3DS XL BLUE with upper screen is IPS and touchscreen TN, and my other EUR N3DS XL BLUE bought last month (9.5FW) have both IPS screen, very very nice.
So for the 4th screen configuration maybe some consoles have only the touchscreen is IPS.
Maybe new consoles are coming with both IPS