1) You can craft them using
Soap + any key. (The soap gets consumed)
But yes a merchant would be nice. One of the fabulous five would make sense.
2) Certain areas have quite a few empty flasks but yes a merchant/crafting recipes for flasks would be nice.
3) The full game will have more companions these are just the ones available in the starting area.
4) last I checked yes you get experience in this case. Likewise you get experience if an NPC kills an enemy