It sounds like you could have multiple issues, so let’s see if we can deal with them, one by one…
First, the Omeprazole - you’re right that many of us with hypothyroidism have too little, rather than too much acid, but we can still have acid reflux, also known as Gastroesophageal Reflux Disease (better known as GERD).
Acid reflux is one of those things that can be present but not really felt, unless symptoms get totally horrible (like I often wake up in the night choking on acid), but sometimes it can be more subtle.
Not everyone with acid reflux has too little acid and sometimes, acid reducers actually work, even if we do have too little acid.
I was on Omeprazole for years for my acid reflux, but it didn’t do much (though I know it helps others). I’ve since been placed on Pantoprazole, which is similar and seems to do better, though there are times I have a lot of breakthrough reflux. For this I drink dill pickle juice (or vinegar and honey in warm water).
There are certain things I can’t eat within 3-4 hrs of bedtime. Those include (but aren’t limited to) chocolate, nuts and caffeine (chocolate has caffeine). We’re all different, so perhaps you could take the Omeprazole, as prescribed, for a couple of months and see if your pain(s) go away. If they don’t, there’s a good chance the doctor would take you off the med anyway.
It’s true that you have to separate your thyroid medication from when you take the Omeprazole because acid reducers prevent thyroid meds (specifically, T4/Levothyroxine medications) from being absorbed properly.
You should try to separate thyroid med (T4) from the Omeprazole by, at least a couple of hours. I keep my T4 med (Levoxyl) next on my night stand and when I wake up around 5:00 am, I take that, then go back to sleep. I usually wake up again about 6:00 - 6:30 and can then have coffee, eat and take other medications. You have to figure how the timing according to your schedule and if work requirements, etc prevent you from spacing out the thyroid med and the Omeprazole, we’d hope your doctor is willing to adjust your thyroid med to accommodate the less absorbance.
Unfortunately, sometimes, taking thyroid meds along with other meds or vitamins/minerals can become a difficult balancing act. We, typically, have to space things throughout the day… for instance, calcium supplements shouldn’t be taken within 4 hrs of thyroid med… Take calcium at noon and at night.
I’m not sure where you saw iron contraindicated. Iron is necessary for proper metabolism of thyroid hormones, but it does need to be separated from them by a few hours. If you’re taking thyroid hormones in the morning, try taking the iron at night.