@Zundalek Zbynek , Following-up on this -
Application Insights Node.js Agent cannot be configured in portal, but it can be configured using JSON file, checkout this article for more info: https://github.com/microsoft/ApplicationInsights-node.js#configuration
JSON need to be part of app and use APPLICATIONINSIGHTS_CONFIGURATION_FILE
to specify the path so Agent can find it. Please try this and let us know, we will be more than happy to assist you further.