Then specifying a header for the system URL (content/view/full/77) and URL alias (/MyFolder) for a node, the header for the URL alias will be used in both cases.

Steps to reproduce

1. Enable custom headers
2. Create a folder, "MyFolder"
3. Apply this configuration (change the node id)

[HTTPHeaderSettings]
CustomHeader=enabled
HeaderList[]=Cache-Control
Cache-Control[/MyFolder]=public,must-revalidate
Cache-Control[/content/view/full/77]=no-cache,must-revalidate

4. Access both URL's, and check the header. URL alias header is always used.