The game has ticks where it runs Be() for all entities. A creature can act on any tick where it has 1000+ Action Points, and with 10 DEX/AGI, that's every 10th tick. So there are 10 sub-turns per turn at the start of the game, but as your stat get higher, you will be able to act more often.
Getting negative experience for hunger/encumbrance is intended and balances out the gains from movement, combat etc. Unless you are constantly Strained and Overfed, you will slowly train AGI; if you want to train it faster, you have to be unencumbered and run around. But as Ischaldirh mentioned, each character gets a modifier that changes the amount of experience needed to level a stat, so some characters will slowly loose AGI if they are burdened, while others will get it quite fast anyway.
No snowballing happens, increased gains of exp are balanced out by diminishing returns at higher stats.
Yup, you can train AGI fast by running in wilderness.
Not sure if that is completely intended, but it works.