I don't know which they are referring to but I would say supplement form would be way worse. I don't think tomatoes are loaded with FOS. However, they do test positive for starch for me here in NZ esp when cooked.
My hubby is very sensitive to starch but he's ok with asparagus and leeks and onions (as long as they test negative for starch as they do test positive at certain times of the year).
Hope that helps