usually you apply the discount at the shopping cart stage, the price is then recalculated at checkout, could be done that way but it's a little cumbersome.
One way to implement a token-based discount is that whoever owns/holds a token gets the discount. Another way (that I had in mind) requires you to transfer it back to the store. In this case it is lot more convenient to transfer both BTC and Counterparty token in the same transaction.
theoritally it's fine to replace the antidust amount sent to the recipipient with any amount larger. However, it's not implemented in the current counterpartyd yet. Maybe later we can customize the amount of BTC we sent in xcp transactions, but I am not sure whether this is really useful.