Because MIT needs to keep its top-ranked football team. 
OK, enough fun. I agree - the people who apply early are a different sample than the people who apply regular. Differences in acceptance rates are driven largely by these differences and not the application cycle.
It’s the same as an SAT. SAT doesn’t really care 780 vs. 800. But the kid who has maxed out all the high school math and is taking the bus so he can take Differential Equations in a nearby college is more likely to get an 800.