I think that the model for project-specific PMD settings vs. global settings is wrong. You should follow what the Eclipse Preferences > Java > Compiler > Errors/Warnings does. This page defines the global behavior. If you want project-specific settings, you click the link at the top, select your project and define the project-specific stuff. When you save this information, it creates/updates a file in the .settings folder of your project. Check it in to your source code repository and everyone has access to the settings.
There is a discussion on this point in the forum titled:
PMD Does Not Respect Eclipse Settings
Discussion: PMD Does Not Respect Eclipse Settings
Discussion: PMD Eclipse Plugin: Check box "Use global rule management"
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