This is a challenging question. So much of this depends on auditor calibration. I've been through well over 100 Food Safety/Quality Systems audits and I've had a few NSF auditors that were laughable because they were so easy and one NSF auditor that was almost impossible to pass with. I have simillar experieces with Steritech, Sillker and SAI Global too.
As for NSF-GFTC, I would have recommended them a few years ago but their really just NSF now. My last three NSF GFTC audits have been NSF contract auditors that know nothing about GFTC.
I would say 98% depends on your auditor. If you get a good auditor recommended, run with it.