Just to add variety, I am the opposite of Bob. I see only one type of flying shoe,
with toe cap. Looking on the Purdue site at
the photo used in the research bulletin to illustrate "pair #1" with smooth toe, I think I see rather clearly both the capped toe and the light-colored inner part of the heel that were noted for "pair 2". For some reason detail is coming out more clearly in the original, on my monitor, than in the photo used in the bulletin. See photo below — but I don't know if all the detail will translate to the forum display software or not.
IMO the only difference between "pair 1" and "pair 2" is that the shoes were still relatively clean and polished in Miami but took quite a beating during the course of the flight.