When it comes to regular initial endo treatments, and non surgical retreatments, I agree that after 2-3 years, it really doesn't matter. However, the one area that I do see a difference is when it comes to SURGICAL retreatments (apicos). The programs where residents get more exposure to doing apico surgeries can make a difference how comfortable/likely the resident will tackle surgeries in their clinical practice especially the more difficult molar cases.
Sadly, I have heard of some programs where residents graduate with no molar surgical experience and shy away from doing any molar surgeries once they graduate. Of course, there are always hands on ce courses an endodontist can take after graduating to acquire more surgical knowledge.