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At the moment the ATO is not data matching with the Custom but it is very likely they will do that in the future.
From a tax prospective whether you pay GST at the custom is irrelevant. Because if you pay it you will get it back on the next BAS. The only difference is the timing of the cash flows.
If you pay a lot of GST at the Custom you may also consider entering into Deferred GST Scheme. This would help you better manage your cash flows.
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