Deffo go back to see your fab GP. It could well be a diary allergy, and yes, one bottle of formula is going to affect a baby with CMPI. The stand-in GP sonds a bit meh, although I think he or she is right to investigate other causes that might present as unsettledness and reflux.
You say your baby hasn't put on weight steadily and has been dropping centiles. Can you say what the pattern's been like - e.g, what did she start on and where is she now, how long did it take her to regain her birthweight, etc.
Have you seen anyone who really knows about breastfeeding to check for milk transfer issues, like poor latch, or tongue tie? If not, I think it would be very useful to do so. Whoever told you that resting is going to sort out your potential milk supply issues is not very knowledgeable about breastfeeding :( Replacing feeds with formula will likely reduce your supply.
I think it's true to say that what looks like reflux (especially of the silent variety) could be caused by hunger, but, it could also be caused by any number of other things....
What symptoms of reflux does your baby have? Is it just the lying down thing, or are there other things too?
If you wanted to try a hydrolysed milk, then you can buy them OTC in boots although they are usually on special order and are £££££. Staydown and anti-reflux milks are not hydrolysed milk products - they still have intact milk proteins in them. Hydrolysates include aptamil pepti, nutramigen. Then there are the elemental milks with no milk protein in them - like neocate and nutramigen AA.
re the ranitidine, I wouldn't think it would take too long to kick in, although if there's damage to the oesophagus it can take a while to heal. I think this'd be unlikely in such a young baby though. It can speed up digestive transit if I remember rightly - perhaps your baby's not happy with that sensation?