They often go together. I think there are lots of reasons for that. Maybe the kid has weak muscle tone to hold down the food. More likely he empties slowly (weak muscles in the GI tract) and so things sit around and come back up. Often there is an underlying issue that is causing the hypotonia and those same issues have GI stuff associated as well.
Does your son have any constipation? Correcting constipation helped my child (mildly hyptonic, severe reflux, dev. delays and issues, failure to thrive) with his reflux. But in his case the underlying issue for both of those things (and his developmental delays too) was metabolic. You've got three metabolic markers there so I'm wondering if you've ever had metabolic (and genetic if there are other markers for that) testing? Here is a link I made about signs of metabolic stuff.
Link Metabolic Information
I'm wondering about some other things as well. Which PPI's has your son tried, is he at proper doses, and is he being dosed three times per day?
http://www.marci-kids.com/dosing.html It wasn't until we followed the guidelines here and switched to Zegerid that we got my son's reflux pain under control and his weight/growth stabilized as a result. Prilosec has compounding stability issues. Many of the meds are underdosed or dosed twice a day which will not help a severe refluxer.
The other possibility is eosinophilic disease. In that the child won't respond (at least not completely) to PPI's because the underlying issue is actually allergic in nature and the treatment is specific to that. My son was scoped to rule it out.
http://www.apfed.org/ee.htm