My guess is that it's because approximately 75% of the male students go to "big schools".
I think the data you have put together and presented here previously has shown this to be the case.
But exactly half of the chances to go to state are with the bigger schools and half are with the smaller schools. Bigger schools do not get to send 20 kids to sectional, they send 14 just like a small school.
If qualifying for state was determined by flipping a coin, then small schools should have the same number of qualifiers. But qualifying for state is determined, in large part, by a person's ability as a wrestler. Based on statistics alone, big schools are more likely to have more wrestlers that have the necessary ability as a wrestler to qualify for state simply because big schools have more people.
For instance a typical big school may have 3-4 state caliber wrestlers while a typical small school may have 0-1. This would make sense because big schools have a more students and therefore are more likely to have more state-caliber athletes. This may be a good argument for why the team tournament should be classed, but it doesn't affect the individual tournament. In the end, for the individual tournament why does it matter what school a person comes from?
Also, under the logic that it's unfair that more state qualifiers come from big schools, it's also unfair that more state placers have come from the Merrillville semi-state in recent years. The Fort Wayne semi-state has the same number of chances for state placers as Merrillville. Should we have a classed system based on geography?
School size is only one advantage, what about better facilities, more paid coaches, less multi-sport athletes, more money for travel to better competition, etc.
These might very well be advantages that some individuals at some big schools have that individuals at small schools don't. There might also be advantages that some individuals at some small schools have that individuals at big schools don't (close-knit communities, family involvement, wrestling families staying in the community, etc.).
Based on the numbers you have posted previously that indicate that the big schools have the same percentage of the total students in the state as they do state qualifiers (it may have been 75% I can't remember, I don't have the numbers in front of me), it seems like the advantages for each balance out. If there was a distinct advantage in being an individual from a big school, you would expect that big schools would have significantly more than 75% of the state qualifiers.
To argue that classing the individual tournament would better the sport is one thing (which I am not convinced would be the case). But trying to twist the numbers to say that individuals from small schools are disadvantaged because small schools don't have 50% of the state qualifiers even though they only have 25% of the total number of students doesn't work.