No comfort for employers
The rules have always been that if your are an employee and you employer deducts tax but fails to pay it on to the tax office, the employee will still get the credits and the ATO will chase the employer. The ATO FAQ simply repeats this.
The employers who paid the gross pay to Plutus as not off the hook. They still owe the tax to the ATO.
Employers are also in a double bind with superannuation contributions. The contributions haven't been paid to the super funds so the employers still have an obligation to make sure they get paid, and because they were not paid on time they are not entitled to a tax deduction for the contribution.