I also faced similar problem.
The project level property added through the script should be shown in the "Custom properties" section and it should be replicated in all the environments. No matter which environment is active.
The moment we add any custom property manually within the tool, it is replicated in all the environments.
I had also given feature request in some other post to provide option for user to Add/Delete/Shuffle (up and down) custom properties in the Environments section, the way we can do in the Project Properties / Custom Properties section (basically providing same menu that are available at the Project Properties section)
Thanks.
