if your GTP is accredited through a university you 'should' be fine. I have a friend who has had her quals accepted recently who did a GTP through a university. I did the same course, so I'm hoping I will be fine too.
You can transfer your quals to a PGCE with some extra work once you have received a GTP, but this is for the school led GTP's, which are not regulated by universities, therefore, have the problem with transference of skills to Australian standards.
If you know you are going to emigrate and have the choice, I would go for the PGCE as there are definitely no problems there. Check that the university give the award and CATS points.
Good luck with whatever you decide.