I wouldn't worry about the system / platform you trade from when...

I wouldn't worry about the system / platform you trade from when considering the issue - the main thing you need have is the correct tax treatment and records to show what you have done.

You would just need to make sure that you don't later forget you are using another system to track your taxable gains when reviewing your gains and losses if your trading platform won't let you pick the parcel you sold for tax purposes.

With you being a share trader on income account (I'm on capital account - I don't tend to trade) you would want to check with the ATO their view in your case - especially if you got yourself a private ruling on the issue.

You would be brave to not apply and follow it correctly given you now have one as it would leave very little to stand on if they reviewed you later and you didn't do what was originally agreed!

Cheers Hevlet