When i was arguing trying to do the same thing (and mind you i had to pay GST in the end as my school wasnt willing to take the chance) we came across the section that says that if you start something in your CPL sylabus but dont complete it by your test, then you may continue after issue of a cpl gst free. I hope that made sense as im going off memory!
What you may be able to argue is (as long as your school agrees) that you actually start your IFR training before you get your GFPT in your instument flying lessons after area solo! 2 hours pre GFPT and 10 hours pre CPL. It depends how chummy you are with your school accountant aswell. But it is definately possible in an interpretive sense. Good luck! And let your school know that if they ever get into trouble later on that you are willing to pay the GST to them. Hopefully that should soothe their minds!
CA