One can always use various ADDLOCAL / REMOVE / etc. properties, which can be passed on the command line. If you're looking for semantic connections, Feature Conditions can change the which side of INSTALLLEVEL the feature rests at based on arbitrary conditions; in this case either command line or app searches, etc., can impact the feature install.
I am going to set some Public properties with a default value. On the parent Features that install by default I will have a Feature condition that will set the Feature Install level to above the Setup Install level if the Public property is different to the default value.
I'll do something similar to the features that don't install by default.
Through using Public Properties it gives the user something simple to change through the command line.
