Can you only get low quality containers here while doing a stockpile during the prologue?

 Not sure, but the prologue should only take an hour or so if you don't take any breaks in between missions. Then you will be able to ramp up the AI difficulty manually and enjoy high quality crates.

Ramp AI? is there a slider or somthing in options to control it?

I didn't see a slider but you can click the gun icon and then the "create" tab, and choose the upwards pointing arrow (I think it was red) to increase the AI difficulty.  I may be off on some of the details as I can't get into the game yet and only just discovered this yesterday.

As soon as I did this, I was able to get high quality loot, though the AI becomes significantly more challenging to a new player like myself.  Prepare to die a lot more vs. mopping the floor with them like you were before.  :)

 To increase AI difficulty manually:

Hit esc--->click on "game"--->at the top should be "PvE difficulty".

There is your setting to change it. Have fun getting high tier crates to make lotsa money.