You could try padding for where the contact is, like moleskin or a bandaid. When the shoes loosen up a bit, and that sore spot gets toughed a bit, they might be just fine.
My feet have become quite sensitive to fit. Rarely do I get shoes that have no break in period for maximum comfort, especially with cycling shoes.
IME, recommendations for cycling shoes, fit wise, are questionable, like cycling shorts. Too many variables in foot size and, more so, foot shape.