I agree with Gorgonzola – they are doing you a favor. You could try to sell the saddle privately, but if it’s a prototype model, it’s going to be tricky. Easier to take the store credit.
Unfortunately, many people do not really understand saddle fit. This board is full of people who purchased saddles that end up not fitting, many of them custom saddles that costs many thousands of dollars – often times because the person advising them didn’t measure their horse correctly or didn’t know how to evaluate fit. Out in the hunt field I’ve stopped telling people that their saddles don’t fit their horses because no one wants to hear it 
until their horse is so sore that they are throwing their hands up in despair.
Many trainers don’t know squat about saddle fit. I had one trainer tell me “for sure” my saddle would never fit my new horse. Saddle fitter felt very differently, thank goodness!
If you can watch a good saddle fitter in action you can learn a lot in a few hours. If you want a good place to start learning about saddle fit, the videos that Schleese has on their YouTube channel are very good. Saddle fitting is not rocket science. Once you know what to look for, you can eliminate the grossly ill fitting ones pretty quickly.
Keep in mind that saddles need to be refitted periodically, too. Horses change shape when they are young, when the amount of work they are in changes, and when they age. It is very possible that during the three months your horse was in regular work, he built muscle over the top line and outgrew the fit of the saddle. My saddles are checked and “tweaked” twice a year to assure that they fit well. Since both of my horses are in middle age and constant work, their shape doesn’t change much but I want to catch anything before it becomes a problem. Often when I’ve had a young/new horse, I start with an inexpensive or adjustable tree saddle because I know their shape will change as they mature.
You haven’t mentioned whether your saddle has wool flocked panels. Sometimes a good fitter can work wonders with adjusting the wool even without widening the tree. Foam panels are meant to adjust to your horse’s shape but after a certain deviation from the norm, they don’t work. I was very frustrated when my TB changed just enough so that my beautiful Stackhouse saddle (foam) no longer fit him; my wool-flocked saddles have proved more adjustable and I personally like the Kieffer adjustable trees, which can be widened or narrowed many times.
I’m sorry you’ve had an expensive lesson in saddle fitting. I hope that with your store credit you are able to find another saddle (maybe a used one?) that is comfortable for you and your horse.
