I tried to cut the seams for the rubber differently, and I got some pretty good results for anyone who's interested in more options. I don't know if this will bite me later in the process, but this looks better than what I achieved previously (first picture shown with the noticeable seam along the tread edge). For this option, make sure you unmark the sharps on the edges of the rubber, shade smooth, and make your seams across the tread, as shown.
This was the question I meant: https://cgcookie.com/community/21165-issue-with-my-model
