I would definitely be pushing the GP to try an alternative dairy free formula where it's more broken down. I think the Pepti one is the least hydrolysed and also the cheapest so more commonly prescribed by GPs (it's also one of the more palatable so this does play a part too).
My little girl was put on Nutramigen just before 6 months after horrendous troubles with wind and reflux. Her reflux was gone in a week and she dropped a nappy size also due to belly bloat disappearing (even though was gaining weight). The wind issues did ease but took 3 weeks before really became apparent.
Like yours, she struggled with food and digestion. I think months of being on dairy formula had taxed her gut. We had a few safe foods - peaches, avocado, porridge (oats with oat milk), coconut yogurt and some vegan and gluten free pancakes. That's all she ate for about a month
Weaning has been a bit stressful with trial and error, but time seems to have helped a lot and she can now have more stuff she couldn't tolerate a few months back - similar with being up for hours in night screaming with wind pain.
We also still give gripe water after her evening bottle and this seems to help with general digestion, stopped it and within a week decided it defo isn't placebo for her!
Around 9-10ish months I think she became more sensitive even to the broken down milk proteins in Nutramigen, with worsening reflux in particular and needing more winding. I thought the reflux was because she was crawling and on all fours all the time and the wind due to introducing new foods. But it all pretty much stopped within a week of switching to oat milk around 12 months and almost dropping a nappy size again after being on cusp of moving to next size up... So not keen on starting the milk ladder just yet.
The only other thing would be to get checked for tongue tie as that can introduce more wind into the system, even with bottle feeding.
I hope you find something that works for you.