I'm convinced they do it purely for the money. Period.
Given most people on our types of medications can't get around that well, it's expensive to see our doctors and get our meds filled as it is, and it puts a huge strain on us to make extra appointments (every 30 days to see our doc to get a hard copy Rx) plus the price of three 30-days is never 1/3 of the 90 day value.
I think they're also trying to make it so difficult, for doctors and patients alike, to try and discourage the Rx of these medications because they are such a bother to maintain. The more challenging they make it, they know already, they're going to be "able to lose patients" who can no longer fill these types of Rx's.
It's a political game of red tape. Kind of like filing for Disability. They figure if they make it hard enough, complicated enough, take away the privileges and benefits and convenience enough, they'll force many patients to d/c this type of care.
Just my $0.02