There is a difference if you choose Out of Scope vs. Exempt as to how it flows onto the HST return. With QuickBooks desktop versions there was no difference, but there is in QBO.
So here is the effect - "Exempt sales (on sales receipts, invoices, credit memos) hit line 101; out of scope sales on the same transaction screens don't. Exempt sales (on JEs, deposits) hit line 101; blank or out of scope on same don't.".
So if you choose Exempt as the tax code for money that comes in, that line flows into your total sales number, even if it isn't a sale. So please take extra care when reviewing the QBO returns to make sure that the sales number you are reporting is correct. A good practice is to run a P&L for the same period to compare the sales being reported on the return through the module.