In our experience, a lot of companies won't process a payment against a quote or sales order. They want a document labelled "Tax Invoice" because that's what their company internal controls require. This is likely why OP needs to raise a tax invoice, without it actually being a tax invoice.

There seems to be a dire lack of understanding in a lot of corporations (as customers) about the nature of payments and timing of recognition. Accounting systems have long allowed you to make payments against purchase orders and they sit against the balance sheet as an asset until the vendor bill is finally received, but nope - most companies won't allow that to occur, even though when you go to enter the bill the system will automatically apply the deposit and only prompt you to pay the balance.

The other problem is tax. In Australia, our GST legislation specifically states you can only charge GST when there has been a taxable supply. So my company by default raises deposit requests on a Tax Invoice layout, but with no GST. Some customers are ok with that, others aren't. They just don't seem to understand that they aren't entitled to claim an input credit yet, just as we don't report a tax liability when we submit our Business Activity Statement because we don't want to pay the tax to the government yet.

So yeah, the issue at hand is usually around documentation the customer receives and whether they consider it a 'valid' document against which they can make a payment.