Don't quote me 'cause I'm just speculating here; an accountant will obviously know the answer but.....
A loss is a loss and a gain is a gain. In a partnership one partner might trade stock the other partner might trade chickens. In regard to the stock and CGT it depends on purpose. ie did you hold the stock as an investment or as a trade. Investment you get the discount; trading you don't.
If you run a business and submit a BAS then I can't see why you couldn't include your stock trading gains and losses each month or statement period like any P & L statement.
The investment stock would need to be recorded in the books somewhere as a holding until sold and the 50% deduction applied in the statement period they were sold. Just my opinion.............
