I also have GERD- and suffer with the same nausea/ vurps type symptoms as Cat. Mine is probably due to a hernia.
I'm guessing that with Crohn's, the ulcers would be deeper in the tissue, since in the intestines Crohn's ulcers start in the middle of the wall and then burst through into the lumen (hole in the middle of the intestine). Whereas ulcers caused by acid would start in the lumen and then tunnel deeper.
Maybe the type of symptoms will also help them differentiate between stomach Crohn's and GERD. Like me and Cat suffer with the feeling of stomach contents coming up, so this suggests that the sphincter at the top of the stomach is not doing it's job, therefore less likely to be directly related to the Crohn's. Whereas heartburn type symptoms could be caused by Crohn's ulcers, and there actually isn't any stomach acid coming up the oesophagus.
Maybe one reason why a lot of Crohn's sufferers have GERD is because the digestive system is more 'sensitive' so even a small amount of acid (which wouldn't bother anyone else) causes ulcerations and discomfort, in the same way as scratchy foods can cause discomfort the other end?
But I agree with the others, you really ought to get a scope. I have been told to use Gaviscon Advance to treat the symptoms, as it's safe to use long term and has less side effects than prescription meds.