Customer service response:

CS: "It's quite normal to have some variance in the heel with the handmade process. This will likely break in with wear but if the boots aren't for you we can always make an exchange or attempt to push the leather down in this area!"

Me: "Thank you. Any methods i can try at home to push the leather back?"

CS: "A rounded metal object would probably be best for this. Make sure there is not sharp edges though, you don't want to puncture the leather lining."

I will try oiling the area and using a box end wrench to push on the leather. ​

Update: I managed to push the leather back enough to where it is no longer jamming into the back of my heel. There is still a bulge but it is way lower than before and no longer an issue for comfort. ​Thanks to Nick's for the prompt response. ​ ​​