1) The stock value you see in your inventory is incorrect - at the moment it still rounds up to the nearest percent (even though 5 stocks is *far* from 1%), on top of which that value is not used at all. The current value of stocks is basically how much someone is willing to pay for them. The value shown in your inventory is how much the faction is worth divided by the number of stocks it has. Not a bug, just two entirely different things.
2) Cross-Terrain XP, like Ascending to atmosphere XP, is limited to 1 XP. All other travel XP is based on the distance traveled. Those two are two entirely different types of travel, and the duration of that travel is not affected by your speed skill, whereas all other travel is. Players have campaigned to have these values increased in the past, but so far they have not been successful.
3) Not at this time, but I believe Khan was going to work on one when he's gotten a few higher priority items out of the way on his massive to-do list.. Hopefully we will see that in the future. (: