In accounting terms, you have two distinct transactions here, that should not be netted against each other.

You have Income in the form of the 'Accommodation Cost' that you provide and on which there is GST payable on your BAS return.

You then have an Expense in the form of 'Commission' (I call it 'Advertising' in my books), which depending on the OTA may or may not have any GST. If the OTA is based abroad like Expedia,, Agoda etc., they are not charging you GST. But if the OTA is Australia based like Jetstar, Roamfree or Quickbeds then there is GST claimable on your BAS return.