PS2013 Library folder inherited permissions

Hello!
I'm planning to create a folder in a library, with special permissions (accessible only by owner and a special AD group). I have created a site template, a library and a folder, where I have set all the permissions and disabled inheritance from parent folder.
Now, when I create a new project and a site for it, this folder starts to inherit the permissions from the parent, so all the planned security crashes and manager has to set up all manually. Is there any way to resolve this issue?
Thank you!

By default, Documents, Issues and Risks inherit permissions from the Project Site.
Whenever the sync job is initiated, these object's permissions will be inherited from the root.
Create another document library and set the custom permissions and observe the behavior.
Cheers. Happy troubleshooting !!! Sriram E - MSFT Enterprise Project Management

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