The calls in the project code CalculateCommonBundles() do not match the calls in ScriptableBuildPipeline DefaultBuildTasks(). E.g. in that implementation CalculateSceneDependencyData is called directly after PostScriptsCallback. We are not able to help debug issues arising with custom implementations that extend the Scriptable Build Pipeline, as it is likely the bug is in the customer project. So it is recommended to compare with the default implementation and see if it is possible to more closely match its order of operations.