We are in the waiver process right now as well for a very mild tree nut issue. Definitely not anaphylaxis but had been documented in records so we had to respond.
As I understand it, up to 30% or more of the class usually have to get some sort of waiver. Some SA's like the USAFA are much more rigid about never giving a waiver for food allergies. Others like USMA and USNA are more flexible depending on the severity. It kind of makes sense as they really want to make sure that their grads are capable of world wide deployment without restriction. You could imagine that you could put both your fellow sailors and marines in jeopardy should your DS/DD have a serious reaction so makes sense for them to be cautious. I don't think the DoDMERB has a lot of flexibility in interpreting the rules thus the DQ's are more rigid. The waivers are determined by physicians at each of the requesting SA or ROTC command and have more flexibility in determining what they will waiver.
My understanding is that the waiver process depends a bit on how competitive your DS/DD are in the applicant pool. If they are not competitive, I don't think getting a waiver is considered. If they are competitive, I think the SAs are much more likely to submit for a waiver review. My DD had gotten an LOA back in December and my understanding is that these applicants are automatically sent for a waiver review which is where we are right now. We had submitted the AMI for this back in December and they had asked for some medical records and such. I understand some others in the past have gone as far as to be requested to have food challenges to document how allergic or lack thereof they are to tree nuts.
Our story is a bit complicated but if you PM me, I am happy to share what information we have. Depending on how many posts you have, you may not be able to PM someone until you make a couple posts but just a quick couple posts should be able to give you that ability.