I am neither an accountant, nor an expert at tax matters.
As a matter of interest the ATO in their CGT calculation examples suggest adding brokerage to the cost base.
From an accounting point, though (note I am not an accountant), the brokerage represents a service cost, and therefore should be treated as an expense, just as bank fees are an expense.
Just because the ATO prefers one method does not imply that is the 'correct' method. It just happens it is to the advantage of the ATO if it is treated as a cost base.
I generally use the cost base method as the idea of getting into an argument with the ATO is altogether too scary.
However I have used the transfer cost (transferring from private holding to super holding) as an expense - indeed the auditor suggested it. As far as I can see the payment for transferring shares from me to me should be treated no differently from transferring shares from you to me. The ATO obviously will tell you to use the cost base as the total amount of tax paid can be greater (when capital gains are taxed at a discounted rate, and expenses are deducted at the standard tax rate).
