Have an OTTB with the typical TB “sensitivities.” Of course, that included the hives. Over the years I tried and have stuck with most of what has already been mentioned. Each step helped a little and now he is rarely hivey:
Witchhazel wash after each ride or right on the hives when bringing him in from turnout. I swear he was allergic to his own sweat (don’t laugh, really. I get a horrid itchy reaction myself in the summer.) he would rub horribly against the stall wall, it was almost a race to get tack off.
Benadryl as needed (usually only once or twice a season, (but I don’t show) when I wanted fast relief. Still keep it on hand but rarely use.
Spirulina. This helped with a LOT with respiratory allergies/cough too.
Allergy tests & shots (until the shots started to cause a local reaction last summer, after 2 1/2 years of treatment. So stopped that so as not to have a worse situation. The shots helped a lot in the beginning but at the end he improved even more when I stopped the shots. Guess that says something, but not sure exactly what. Vet said 3 year course is pretty standard, so I guess we got the most we could in the 2 1/2 years.)
Acupuncture/chiro partly just because he was quite crab for a while and just seemed uncomfortable for no specific reason. Ya I know, allergies can make you feel like crap BTDT.
Chinese herbs, a shot course when he was reacting to the allergy shots. (I’ve kept up the accu/chiro - wonder if the DVM you refer to is the same one I use,; he spends part of his time in AZ and part in MI. Great guy!) The herbs were too pricy for me to keep up and frankly they were the one thing I didn’t see him helping at all.
Flax seed. Switched from long term cocosoya use. Don’t think he was soy reactive, mosttly a matter of price, convenience and just thinking of what else can I try.
All of the above have helped improve things step by step and my horse is still on all of them except the shots and herbs. He also gets MSM for other reasons.
A bit over a year ago, I put the Fjord who rubs his hind end and mane only during the summer (May-Sept/Oct, so I think it’s bug related) on spirulina and flax seed. Major improvement, lots less rubbing.
One other thing you mentioned popped up the red flag for me. You use natural fly spray. I did too, except under the worst conditions. Most are citronella based I liked them for a long time, then about 2 years ago my OTTB got hives when sprayed with them. I could see the pattern if I just did certain areas. Once he got sensitive, this was the worst trigger of all. So do a little test and see if that may be an issue for your horse. Now I use lavender water (SIL has a lavender farm & had a customer ask her about it, so she asked me to test it out & of course I have a for life free supply that helps.) when the bugs aren’t too bad. It doesn’t really hold them off in the worse time. At that point I judiciously pull out the Bite-Free to knock them down. I like to use as little chemical spray as possible. If you read the labels and know what they mean all of them have the same major class of chemical as the main active ingredient and it’s one that insects develop resistance to quite fast. (Won’t give you the long story or get on my soap box, but have long experience in another part of my life/career. You can PM if you want it.)
So watch the citronella (and some other herbals that can be quite irritating to skin.)
Good luck it’s a struggle at times but as you get all the details in place hopefully it improves. (I also use fly predators and OCD manure management to keep the flies down since I have my horses at home. Prevention=Best cure:D.)