I guess this is my truly first time when I took some open source code and added feature that I was missing. That's quite an interesting feeling that you have influence on how things are. You can change something. And someone else can benefit from that as well.

Anyways.

You can download fixed plugin here: https://github.com/max-kviatkouski/intellij-micropython/releases/tag/1.0.6-fix-pyboard-excludes (it includes description of the fix and example of use)

Pull request has been submitted so hopefully fix will be available soon in official distribution of the plugin.