Hey Major,
Been tied up most of the day.
It sounds like you've made a lot of progress in your healing, and hopefully your doc has you doing the right things at this stage of your recovery so not to have a setback. I'd have probably kept you in the cast another 2 weeks just to give the fracture a little extra time to consolidate, to be on the safe side, but maybe it looked good enough at 4 weeks for him to feel you were ready. Without seeing your foot and your x-rays, I cannot say he was necessarily right or wrong. If running in place does not aggravate it, that's a pretty good sign that the fracture is well along in the healing.
I think one of the big things that has to be evaluated when you get to the point you're at is what was the actual reason or reasons that the 3rd metatarsal developed the stress fracture in the first place. This is not always that obvious. You may, or may not have been overtraining, but even if you were, that likely exposed an underlying weakness or vulnerability predisposing you to this injury. Determining the underlying cause(s) needs to be carefully evaluated and addressed to reduce the likelihood of a recurrence of this or another related injury as you get back into running. Things like footwear, vitamin D levels, bone density, foot structure and alignment, structural and functional asymmetries of the lower extremities, and training habits should all be given careful consideration. This would likely involve a comprehensive medical history, biomechanical workup by a sports physical therapist, and further studies such as bloodwork and bone density testing if thought warranted.
If your foot is still bothering you, that does not necessarily mean a cast is in order, but a very careful and complete evaluation has to be made, and this may require another MRI, to determine just exactly what it is, and what it is not, that is keeping it painful at this point in time, and then treat the issue(s) accordingly.
I've seen x-rays many years after-the-fact where the area of a fracture had healed but was subjected to an unstable healing environment (no immobilization), which resulted in a bulbous appearing enlargement of the bone. That does not automatically mean there will be permanent discomfort as a result, in fact, usually there is not any residual discomfort if that fracture has fully healed. If there is discomfort, however, it is likely either that the bone still isn't completely healed, or that it is applying pressure on an adjacent structure.
If excess bone formation was placing pain producing pressure on the adjacent muscle or nerve tissue, this bone could be surgically shaved away, which may do the trick (no guarantees in surgery, as scar tissue and chronic pressure on nerves can cause permanent damage in some cases). If that was going on in your case, it would be very obvious when looking at your x-ray. I mean, it would look really abnormal, and stick out like a sore thumb visually, so if your x-rays don't appear that way, ie, the bone contours of the 3rd metatarsal looks like those of the adjacent metatarsals, this is not what's happening. Also, if it were the case, you'd typically feel decent sized lump over the metatarsal at the fracture site.