Change to workspace behaviour.
Current design:
The Lightweight checkout for Pipeline (using the 'Pipeline script from SCM' option) uses a Temporary workspace. The Temporary workspace syncs the Jenkinsfile Script into the @Script directory, but then continues to use it for the Implicit checkout step (assuming you declarative).
Proposed design:
Auto delete the temporary workspace for the Jenkinsfile Script checkout. Create a workspace based on the name format field in the configuration for the implisit checkout step.