So I was going through some failed ironman characters to look at gear, stats, feats etc. and while I was messing around with these characters I noticed two things.
The first thing was that having on over 100% armor penalty put my stealth skill into the negatives, which I found very odd since I assumed it capped at 0. This made me start messing around to see how armor penalty affected other things. I noticed on one character that his movement points were not what I expected. 6 Agi, 37 movement points without armor on. This made me very confused and so I started messing around with different starting characters and their agility points to see if the formula on the wiki (AGI-5)*3+30 was incorrect.
After making several different test characters with different agi I realized that the original character had nimble and thus a negative armor penalty and so he had bonus movement points. I checked with stealth, dodge, and evasion and it seemed that none of those skills were affected by negative armor penalty. Interesting stuff.