Yes, rosdep will not "see" the directory (or any sub directories) in which the CATKIN_IGNORE file is located and thus will not consider it when looking for and parsing package manifests.
I'm not exactly sure how you intend to use CATKIN_IGNORE with rosdep in the context of developing for multiple ROS versions. Are you maintaining two versions of the same package as siblings (ie: in the same workspace and/or repository)?