I understand your concerned, as I have referred this to customs, there are few options for acknowledge the rates apply (gst or zero-rated or exempt) either you put as the indicator or special code refers to the rate apply. As for me, I prefer to put it as code indicator such as SR for gst charges.
As Tut already mentions about the system, to make it easier for me I just mentioned the code in my item code. So far, I have no issue with the invoices and they are satisfied enough with my monthly statements
You can double confirm with them to get a better picture about it.