Similar to overpaying tax in the UK for not completing a whole tax year, it will happen in Australia. From whenever you sign on until the last day of June your tax will be deducted as if equal across 26 payments.
ATO isn’t as scummy/thieving/deceptive or treacherous as HMRC. You will get your overpaid tax back easily and quickly on your 1st return.
Should you wish to use it to cover the unused portion of your Concessional Contributions which rolls forward into new tax years. Talk to your agent before you submit your 1st return, they may suggest you should complete a notice-of-intent-to-claim or a variation.