1. Your functional medicine doctor sounds OK, like s/he may know what they re talking about. Very hard to find a decent one...so I would be inclined to trust and work with this practitoner. They advice and meds you got are solid.
2. I'm not a big believer in diagnostic tests...they often are wrong, but yours show a pretty clear portrait of low cortisol. Taking thyroid meds unnecessarily can be very stimulating and exhausting to the adrenal glands. Its probably good you stopped.
3. Pregnenolone is an appropriate treatment, I think. It'was very stimulating for me the first few days but then it smoothed out and became supportive and mellow. Give it a chance. It helps the production of cortisol.
Licorice can stop cortisol from being broken down. It can give endurance and support.
In summary, you are an unusual case of someone working with a doctor who 'gets it' and I would work with them and trust their advice unless it starts to do you clear cut harm or make absolutely no sense.