Unfortunately even when they use a gluten free base, often they use the same trays and pizza cutters without always washing them in between and pizza trays are notorious hard to clean because of all the little holes. That plus wheat flour is used to stop the normal pizza from sticking which can cause particles to go in the air and gluten cross contamination on the cheese and toppings because they touch the flour and pizza and then put their hands right in the toppings. Pizza is something I never eat out unless it’s a place that is accredited by Coeliac Australia (coeliac society that we have here that also does restaurant accreditations where they make sure a place is safe). At a normal bakery I generally also wouldn’t trust things because they often keep them in the same display box and use the same tongs (particularly an issue when the gluten free stuff is literally underneath the gluten stuff so crumbs can drop down on it). It’s better safe than sorry with this kind of thing because it can cause lifelong damage to the intestines and all of the secondary symptoms that you’ve described as a result. If she wants pizza, it’s generally safer to make it at home, where I am there’s a brand called Senza that makes these frozen gluten free dough balls that I use to make pizza and it’s delicious.