My company is switching from Eclipse to IntelliJ. In Eclipse we had a following configuration for suppression filters in checkstyle.xml
The Checkstyle integration in Eclipse is more powerful in some respects than the one in IntelliJ. This is one such case, I believe.
I would recommend changing the Checkstyle setup so that you have only one Checkstyle configuration and a central suppressions file for all modules. As you will see, modules are more tightly related in IntelliJ than projects are in Eclipse, so this is actually a good idea.
In order to keep module-specific configuration and/or suppressions, you would have to do the following:
This is quite a lot of work though, so I think you will find centralizing the configuration more convenient. (By the way, here are the supported variables, none of which will help you, I'm afraid.)
Thanks to Thomas Jensen's answer, I solved my very same problem. I answered in detail in this question. Hope it helps.