1) Average of Agility and Strength, not just Agility - and they reduce the overall penalty, just as ranks in the skill reduces the overall penalty.
3) No, the stat bonuses will not reduce the minimum penalty. Strength, by itself, can reduce that minimum penalty, but only if you are using the Encumbrance rules found on RMC Character Law, page 142 (there is another set of Encumbrance Rules (found on Table 10-04 on RMC Character Law, page 137) where the Strength stats does not modify the Encumbrance modifiers (and thus does not modify the minimum armor modifiers either).