So that means that the character is more skilled with armor than without it? Isn't it odd?
No, it means that even though you're taking the full minimum penalty, your combined stat bonus is high enough that overall you get a bonus instead. Your character is simply Agile and Quick enough that the maneuver penalty no longer matters as much: it is still used as part of the calculation. And again, the Armor skill penalizing its purpose does not make sense.
But, using my preceding example, it means that I'm applying the Ag bonus twice for some stats (if the MP is positive), since the Armor "skill" uses Ag bonus.
Also, if I can apply positive values to stats using Ag and Qu bonus while wearing armor, what prevents me from boosting the armor "skill" with a few more ranks (wearing the same armor) in order to get a better skill mod?
The way the skill is written, in my view, even though the total armor skill mod would be positive, there is an upper bound to respect (i. e. -6 for soft leather).
Sorry, it looks like I answered my own question
, but I still would like to have other people's view.