Clayton’s email to Anderson describes that Holman “was provided a vehicle to use during his employment at T3, but Mark indicated that none of the student-athletes have been provided transportation to eliminate any scrutiny of doing so.”
It does not appear, given the prior awareness of MU staffers, that the housing and use of a vehicle would have been considered impermissible benefits by themselves. But it seems they became viewed that way after the NCAA and school in their review determined that the players had been compensated “for work-not-performed at a business through a summer internship program,” as stated in Missouri’s release.
http://www.columbiatribune.com/sports/mu_basketball/banned-missouri-booster-says-he-meant-no-harm/article_6c7158b1-5102-58fe-bdb1-c06c36aeacc1.html
Holman was the student manager that also participated in the internship.
What you are detailing are impermissible benefits, not payments. They weren't 'paid' differently for participating in the internships. The first group of Clarkson, Criswell and Bolton arrived in Georgia with no money so Tuley arranged for them to have cash provided for gas and food. That is the reason for the discrepancy in impermissible benefits between the two summers.