Running Drupal code inspections via PHP Storm returns incorrect results
OK - Embarrassingly enough, this was indeed "user error". The path to the coding standard that PHP Storm was using was indeed slightly different than the path I thought it was using. The paths were quite similar so I didn't catch it during my own reviews.

What helped is that you can configure PHP Storm to output the exact command it runs in the debug log by doing the following: Open Help > Debug Log Settings and add there com.jetbrains.php. Then run the inspection and look at the debug log.