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rosdep is a front-end to package managers like apt, pip, macports, yum, etc... It (generally) does not attempt to look for your own source-based installations. Thus, if you've installed the system dependencies yourself, you don't need to use rosdep, in the same way that you don't need to use apt.

If the dependencies aren't being located, then you'll need to look in:

1. the tinyxml and yamlcpp ROS packages and see if the manifest.xml is correctly forwarding the flags (look for the <cpp> export)
2. the CMakeLists.txt build files of the things that are failing to build to see if they are linking improperly

In ROS Electric, we started transitioning both tinyxml and yamlcpp to system dependencies, which is why there are two places to look. In future releases, it will just be #2.