Illuminated Cloud doesn't currently update package.xml files at the child metadata type-level. It can maintain entries at the level associated with files in the filesystem, but not based on the contents of those files. As a result, right now it won't automatically add/remove entries based on distinct custom label entries of custom labels files, fields of standard/custom objects, etc.
For example option Add to Metadata Subscription... adds all CustomLabels as follows:
<types> <members>CustomLabels</members> <name>CustomLabels</name> </types>
I would be great if we can achieve package.xml as follows:
<types> <members>My_First_Custom_Label</members> <members>My_Second_Custom_Label</members> <name>CustomLabel</name> </types>
IMHO nice approach would be additional menu with ability to choose child-level metadata like labels or fields displayed according to context of parent metadata file that we want to Add to Metadata Subsctiption....