You might have passed the first of many hurdles but that would not stop them as assessing you as a “training risk”.
And just depending what has been identified as SERIOUS ISSUES might be their way of saying, yes you might achieve licence issue, but you are potentially unemployable due to the “issues”??
The ATO exists as a business to make profit and return dividends to the shareholders.
You as the potential customer must be fully aware of the coded messages made by the ATO.
Take the 16PF test independently with a qualified psychologist for a second opinion.
You must be able to pass the “beer test” comfortably.