Hello,
Well it sounds like you are addressing many of the usual suspects. I would say at this point that you call your vet back and tell them what’s going on. If you were my client I would recommend a recheck to include a rectal exam for anal sacs (some refill in a matter of weeks) a rectal exam of the colon (for masses or abnormalities causing discomfort), a thorough check for fleas (and to make sure Parasiticides are being given appropriately), and a talk about allergies with better medication options given to help eradicate the itch. This is where I would start. Yo it dog is either uncomfortable or itchy. Check again and try to rule out one versus the other. Also if they are scoring to the point of trauma to the skin you may need an antibiotic or topical treatment for the skin in the urogenital/rectal area. Let me know what happens. Good luck.
Maybe you can talk to your vet about a long term sensitive stomach food to try? Or make sure it doesn’t correlate with any of the preventatives you give. (And if you’re aren’t giving them you should check to make sure it isn’t intestinal worms with a fecal sent to the lab for analysis). Also some dogs benefit from probiotics long term and gi protectants. I can’t tell you what’s going on with your pup but I do think there are lots of low cost options to try to figure out what it might be. Also you should remove all snacks and treats for a month or two to see if this helps. I worry about gi issues and pancreatitis. In some cases there is excessive gas so a diet change might help. Talk to your vet about all of these. Let me know what happens. Good luck.