It doesn't affect his eligibility.
It's not like he was paid him to run in the singlet.
As someone said in the other thread
http://www.letsrun.com/forum/flat_read.php?thread=2492076
if it affected his eligibility it would mean you'd have to run without any logo what so ever on the jersey if you were racing in the summer or redshirting.
All those races Rupp ran in the Lance Armstrong Nike singlets in Europe would mean he's ineligible.
Perhaps if you want to say he's ineligible you should argue the opposite, not that he was a professional but that the singlets are so rare, it's an illegal benefit.