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(I'm going to post this as an answer, but it's really more a summary of the discussion in the comments)

What you're asking for is not possible afaik: Catkin will only generate a single pkg config file for a ROS package. It's not possible to have it generate multiple files (for separate targets fi).

It's actually the catkin_package(..) call that (eventually) generates the config file and the config file generated will contain information on all libraries added to the LIBRARIES argument of the catkin_package(..) call (and conversely: if you don't list a library there, it will not be mentioned in the pkg config file).