You are correct. Having coached high school teams, I can attest that talent varies greatly. Some kids do nothing and run 16:30 while others run all summer and put in 50mpw during season only to run 19:30. Then there is the kid who trains relatively well and he runs 15:10.
Some D3 guys are way more into running than their D1 counterparts and they put in 100 mike weeks, they eat well, sleep well, lift, study the sport, but never break 15. Their talented high school buddy goes D1, drinks, goofs off, doesn't run in the summer, doesn't eat well, and only runs to keep his scholarship going. He runs 13:55. Talent can't be beaten.