To properly fix this issue JDialog extend in https://github.com/magento/magento2-phpstorm-plugin/blob/5.3.0-develop/src/com/magento/idea/magento2plugin/actions/generation/dialog/AbstractDialog.java#L38 has to be replaced by DialogWrapper:
https://plugins.jetbrains.com/docs/intellij/dialog-wrapper.html?from=jetbrains.org#examples

Based on the answer from the official support: https://intellij-support.jetbrains.com/hc/en-us/community/posts/14397678486418--Thread-context-was-already-set-CoroutineName-commit-workflow-when-showing-window-during-commit-check?page=1#community_comment_15082225353874

Here is an implementation from other plugin: jshiell/checkstyle-idea@8102396

This is going to close ~60 bug reports.