Here is why it's important to set the root priority on the 2 core switches- it means that if you later replace the 3560 with a switch that happens to have a lower MAC address, the root won't change. This could also happen if you add another switch that connects to the core. The greatest cause of instability on a spanning-tree network is the lack of a predictable root.
Imagine what your spanning-tree design if you were to add another switch and IT became the root? Where would blocking occur? The answer is, it depends. Even modifying the port cost the way you were thinking about would not guarantee that blocking would continue to happen as you want. Set your primary and secondary root and then relax with a cup of coffee.