There are different types of "clearance" measurements as some of the other members here have pointed out. The most common clearance measurement is called "running" clearance, often advertised incorrectly (or covertly) by manufactures as "ground clearance" or just "clearance". I believe the manufacture spec for the LC100 quotes "running clearance" to be 9.8". while the GROUND clearance is 8.9".
Running clearance is the distance between a level ground surface and the lowest point on the vehicle excluding ALL unsprung weight. IE this would exclude the wheels, brakes, hubs, axles, and most importantly the rear diff for us 100 guys. I measured about 9.8" from the ground to the bottom of the factory side steps in the "N" height for my ACH equipped 100 on factory equipped 31" tires.
GROUND clearance on the other hand, is the distance between a level ground surface and the lowest point on the vehicle excluding wheels, brakes, and hubs. IE this measurement would measure from the rear differential (as this is the actual lowest point on the vehicle) to the ground and would be slightly less than the "running clearance" previously mentioned. As the OP mentioned, I also measured this distance to be about 8.9-9" from the ground to the bottom of the rear diff case.
Hope this helps clear things up!