Has anyone heard of a medical waiver being passed through Cadet Command for Eosinophilic Esophagitis?

As a former HRT in an ROTC program, immediately tell the PMS that Yes you want the Cmd Surgeon to reconsider the application for "Medical Determination" which is the terminology if you are a contracted cadet- versus not yet enlisted-and signed a DD4 Enlistment Contract. Tell him/her you will get a second opinion from a Dr. specializing in Internal Medicine and re-apply as soon as you can. You might get a Dr. appt BEFORE talking w/the PMS so you can 1) show you're on top of the situation & 2) that it will be taken care of expeditiously. Do that now & I'll draft more information for you. By the way, what school are you attending?

I've never heard of a waiver being granted for EoE because it's one of those "can't be cured, only mitigated" type of diseases. I've known a few with EoE in the military, but that's because the "get in the military medical standards" are tougher than the "remain in the military medical standards".

DoD states that the standards* are to ensure that individuals considered for appointment, enlistment, or induction into the Military Services are:
(1) Free of contagious diseases that may endanger the health of other personnel.
(2) Free of medical conditions or physical defects that may reasonably be expected to require excessive time lost from duty for necessary treatment or hospitalization, or may result in separation from the Military Service for medical unfitness.
(3) Medically capable of satisfactorily completing required training and initial period of contracted service.
(4) Medically adaptable to the military environment without geographical area limitations.
(5) Medically capable of performing duties without aggravating existing physical defects or medical conditions.

Specific to you, your best bet is if you can submit evidence mitigating #2 and #4 either because you know what sets off your EoE (i.e., you have a food allergy to shellfish which heightens your gastric response, etc) and can easily avoid it, have it easily under control with common medication available worldwide, that not having that medication available for an extended period of time won't cause an issue, etc.

I'm not saying that your waiver will be approved if you do all this, just that it will be your best shot at getting one approved. You need to give a 'warm fuzzy' to the waiver authority that YOU should be granted a waiver because YOU'RE not going to be an issue with any of the above categories.
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* DoDI 6130.03-V1, March 30, 2018

History of Eosinophilic Esophagitis is a PDQ per DoDI (Department of Defense Instructions) 6130.03. If you look up that DoDI, you will find it in Section 6.12 , Subsection a4. That's why your waiver came back denied. Honestly, I'm surprised the waiver request was even sent up.