It actually is annoying me thinking about this. I assumed that I could exit regardless of the amount of BTS or bitUSD held in my account * as long as my collateral can cover any loss.
Having shorted stocks before, I'm actually credited the amount of money for the shares I shorted. I can then use that money to buy back the shares in order to close the position out. I don't ever have to go to the bank and transfer more money in to buy them back. But I also can't use that money to buy other stocks if it puts me over a required margin amount.
Why can't I be in control of the BTS from the sale of the bitUSD? I know it will mess up the 3x collateral claims, but I think 2x collateral is plenty. If not, you need to implement a manual cover that will execute at limit orders and not be shuffled to the back of the book.