Hi jppavone,
I see you're looking for info on handling a novated lease and adjusting the tax taken for your employee for the last financial year. I found this thread that might help you out with the novated lease part.
For fixing the EOFY finalisation, you can undo the finalisation, change the ATO reporting category for the payroll categories you've set up, and send an update event before refinalising your EOFY. This will update the tax calculated on the employee's Income statement.
Feel free to get in touch if you need more help.
Cheers,
Princess