If we go by a definition based on actions, rather than skills, I think this problem goes away:

Let's define an action as instrumentally rational if it brings you closer to your goal. Let's define an action as epistemicly rationality if it brings your mental model of reality closer to reality itself.

Those are the definitions which I generally use and find useful, and I think they successfully sidestep your problems.

The question then remains how does one define rational skills. However, answering that question is less of an issue once you know what actions are instrumentally/epistemicly rational. If you may want to learn a skill, it is possible to ask whether the action of learning that skill falls under the categories mentioned above.