Bottom line is mostly won't affect where you can do fellowship training, but that it will affect where you can work. ie, as a 3yr grad, I doubt you'd ever be allowed to work shifts where you're supervising residents with more experience than you.
My alma mater accepted 3yr grads as fellows, but they couldn't work shifts at our teaching hospitals, but instead worked at other hospitals staffed by the physician group, but not residents. From personal experience, all the fresh 3yr grads I worked with at our community hospital were very capable and very smart, but it did feel a little odd sometimes presenting patients to someone who sometimes had less clinical experience than me when I was a senior resident. Not necessarily bad, just odd.