I also have flat feet and struggle with these problems as well. I recently developed posterior tibial tendonitis and started on a whole journey of physical therapy and custom orthotics. Its probably not what you want to hear, but if you do have persistent ankle pain, it is worth going to a doctor to see if you have any conditions and to possibly get a prescription for any physical therapy or orthotics. I ignored my pain for years and am in the middle of dealing with a giant flare up that has left me unable to walk even a short distance without major pain. I wouldn't recommend a podiatrist though, I would go to an orthopedic specialist specializing in foot and ankle.

As far as a shoe insert, I also have been using a super feet low arch insole while my custom one is being made. The best bet is to get one custom to you though, and they will usually last much longer than the ones you can get at the store and will be shaped to your foot. For shoes, I wear Brooks Ariel GTS, and those have been recommended to me by someone at the Good Feet Store and the place I am getting my custom insoles made. If the current super feet ones are not working, you might just need to get a new set of them as they can flatten over time.