Hi Maksym,
What you are describing doesn’t look like an expected behaviour. The plugin extends the branch spec, but doesn’t replace it. Basically you don’t have to have a branch spec of refs/pull/*/head configured for the plugin to work (and if you do, all PR branches will be used, not only ones filtered by the plugin), but any other branch specs should be just fine. So in your case it could be a bug in the plugin or a case of misconfiguration.
Would you mind to create an issue on our issue tracker here: https://youtrack.jetbrains.com/issues/TW and provide exact desribtion of it, i.e. a default branch, exact branch specs, your triggers configuration including the branch filter in it (if any), the configuration of the pull requests build feature, what you percieve as “not working” (not detecting changes, not triggering builds?) and anything else you consider relevant. Thanks!