Good question.
<script> is the compiler-generated function that performs the project’s initial setup. It runs once to load imports, define classes, methods and globals, and execute any top-level code.
After that function returns, the VM creates the App instance and fires its Run event. That event is internally called App.$handler_Run, which is why the two appear as separate roots in the call tree. The small amount of time attributed to <script> is normal startup overhead.
These names expose more compiler detail than is useful, so I’ve improved them for the next release. <script> will appear as Project startup, while App.$handler_Run will appear as App.Run. Other event handlers will receive the same cleanup.