It should be fairly accurate at 2 yrs old. It's more accurate after 4, but most people I know got a good idea of their child's allergies at 2, especially food allergies. My allergist was pretty thorough and I didn't feel like I needed to question him much. He asked about all kinds of symptoms, and even told me to bring my 2 yo back when he's 4 b/c he has "allergy eyes." Ds tested neg to everything, but the allergist said environmental allergies don't often show up in tests until after 4 years of age.
I'm not sure if I have any suggestions for ?'s to ask.
As for her gut, what kind of symptoms does she have? Is she on good probiotics? IME/IMO, food allergies can cause irritation in the gut, which can lead to imbalances in the flora. Also, conversely, gut flora imbalances can lead to food intolerances. Either way, avoiding foods that seem to affect her adversely and taking good probiotics should help her. If she DOES have food allergies, to make her chances of outgrowing better, you need to avoid even traces of the offending food for at least 6 mos to a year. Talk to your allergist about this. Sometimes they will say a mild allergy doesn't warrant total avoidance, but they're used to dealing w/ families who are too lazy. If you tell him/her you are willing to avoid 100% to help her outgrow, s/he will probably be more willing to share good info w/ you. I think they get discouraged dealing w/ the average mainstream don't want to be inconvenienced parents and quit trying to push total avoidance. In my experience anyway. And we already know you put your kids way above inconvenience anyday.
I hope your allergist is a good one! (In a crossing my fingers for you kind of way.
We all know how docs are... you never know what you're gonna get.)
Hope you finally get some answers!