I don't see any contradiction between these paragraphs.
The first says that you can't use the same ability twice simultaneously. eg you want your hero to jump over a small wall and attack a defender. You decide that the important fact is to make it over the wall and so choose Jump as you lead ability. You Can then augment with Strong (useful for jumping) and you combat skills. What you can't do is to augment your combat with Strong as well.
What the second paragraph says is that some skills need no effort to use. ie your Strong is automatically on, however your Hate Guards skill will need an action to activate, ie it takes some time to "work up your hatred".
There is no conflict. Inherent characteristics are "always on" and used all the time.
I have common abilities already listed with their auto augments. eg combat abilities, including weapons, armour, and inherent characteristics, the only thing that my players have to add is any magic.
Hope this helps.
Gavain
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