The single best study on this issue is here, with a related commentary here.
The take home message seems to be that children/young adults with ASD have no greater rates of gastrointestinal symptoms, such as diarrhea, gastroesophageal reflux and vomiting or abdominal discomfort and irritability.
Children/young adults with ASD had a higher incidence of constipation and feeding issues/food selectivity.
This seems likely to be caused by two factors:
"The ritualistic tendencies, need for routine, and insistence on sameness that are characteristic of children with autism may lead these children to choose and demand stereotyped diets that may result in an inadequate intake of fiber, fluids, and other food constituents."
And
Effects on appetite are known adverse effect of medications commonly used to manage some ASD related symptoms.
There are sub groups for which this does apply, females with Rett Syndrome for example but in general, there seems little reason to think digestive problems are more common in people with ASD.
Re: Derrick MacFabe
His group certainly have a hypothesis related to ASD and the gut.
But his published work to date has all been injecting rat brains with high levels of dietary acids and thus recording neurological symptoms, some of which (not all), are ASD like.
Considering how well the liver gets rid of these things, add in the blood-brain barrier and you don't have much to run with.