There is a enhancement logged for this..am afraid this is still in the internal review..
you may add your company details to the bug
Bug 7626911 : THE BILL CANNOT CONTAIN ITEM TRACKED IN TWO QUANTITIES.
Thanks for the response.
What would be some alternatives that we can explore other than alternate bill.
sorry that I come back to this older ticket from you, but I am curious whether you found a solution meanwhile? Seems we hit the same issue and I see that the enhancement request is not moving forward, like almost all ERs.