Neither the FAA nor the AME (who may be thought of as a sort of designee) are actively TRYING to disqualify you. Nearly 5% of adults have hypothyroidism.
https://magazine.medlineplus.gov/art...n%20in%20women.
In this day and age, it’s generally easy to treat. The big problem with routine medications is compliance. 50% of people on chronic medication don’t take them properly or get proper follow up.
https://www.uspharmacist.com/article...tic%20efficacy.

Call it “due diligence” or just covering their @$$, neither the AME nor the FAA want to take the liability of you being in that 50% on your word alone. It’s nothing personal, it’s just they have seen to many treatment failures due to noncompliance.

if you just show you are getting the appropriate treatment and follow up (even routine medication doses can change with age, weight, and diet), there should be no problem. All the CACI stuff was delegated to the AMEs because it was pretty straightforward and routine - to the point it was really a waste of time for OKC to routinely be involved.