I am sorry this unfolded the way it did. I suspect someone reviewing medical paperwork finally noticed “needs extra time for tests” and made the connection to the likelihood of a formal 504 plan and a possible history of a spectrum or similar diagnosis, which was not reported. Those are roadblocks for accession to military service. Waiver policies differ by service, because service missions, operating environments, gear, etc., differ, and the waiver process takes time, additional medical information, levels of review.
The accession bar for medical standards to enter the military is set very high for a reason. The military often operates in harsh, remote conditions, far from advanced medical help, in enormously stressful and often dangerous conditions. The unit’s safety depends on the individual health and readiness of everyone in the unit. Officers must look after their people and may be called upon to make split-second decisions that can be the difference between life and death. There are wonderful candidates each year who have a history of something that would not prevent them from entering almost any other career except the military. The people who ran the program at the local level - their hands were tied once they realized what factors were involved. The military is a utilitarian organization - the good of the many outweighs the good of the few.
Here’s what I think is the current accession standard reference. Section 5.28.