Physicians tend to order imaging instead of relying on the results of a good physical exam (often resulting in unnecessary costs). This is not a knock on them. There is so much pressure on them by their patients, such as yourself, to quickly find a "cause" of their ailment.
If the x-ray is clean and the PTs you saw believe it to be due to soft tissue instead of bone then it's a good chance (but not 100%) that it's probably not a stress fracture. On the other hand, MRI's are more accurate and you would be able to know if you have a stress fracture (if piece of mind is your end game).
Further food for thought: If the MRI comes back positive you will have to take a few weeks off to let the fracture heal, but since you are in that much pain wouldn't a few weeks off benefit your foot either way??? I know of way too many college and high school athletes, particularly runners, who get all sorts of imaging (MRI and xray) just for piece of mind when the obvious course of action is to back off the training load or take a few weeks off. The coaches are also to blame. What a waste of money.