Which years are you talking about? Which tire size on the 2 models you are comparing?
Ground clearance really is from the floor to the lowest point under the car. Usually a differential. The only thing that can increase that clearance is taller tires. The lancruiser has different tire sizes available but they equates on both lexus and landcruiser to about 30.5". Now depending on the tire brand that 265/60/18 or 265/65/17 could be 30.6 or 30.8, or 30.4 etc... so technically in a math class 30.65 is taller that 30.49 but....hardly. in real life not noticeable.
Then after that maybe the lexus has lower hanging front bumper....or cool go fast looking front spoiler and low hanging side steps.