Workspace plugin doesn't work as expected

I'm just trying out the new Workspace feature of intellij (in IntelliJ 2024.3 RC). I found that all my run configurations are broken, as they use the workspace directory and not the project directory as working directory. Specially, as i use .env files for setting environment variables, the location of the .env-file points to the wrong directory. I expect that my run configurations aren't touched. I don't find any option to control the behavior of the plugin. How can I ensure, that my run configurations point to the correct working directory?