I don't know PA, because I couldn't understand your summarization.

The old formula was essentially something along the lines of (combined negative bonuses) ^ (ATIT), I believe it is now 1 / ( 1 / (combined negative bonuses) * ATIT). That is my basic understanding, it could be wrong though.

I'm still non-the-wiser then lol

SAL already answered your question - AT will still make negative mods become more negative, however they won't be as negative as before (note there will likely need to be some re balancing for stealth augmenters).

Why not make Stealth POSITIVE? The larger the Stealth number to more Stealthy you are.

I.e., a ship that is Stealth 100 would be 100% invisible.

because then all stealth augs would have to made into positive numbers and have really small values