heycal, I'm having some trouble imagining the location of the two pain areas you're describing. "Upper lumbar/lower thoracic region" seems vaguely in the same area as "middle/upper lumbar area" to me. Is the latter a tad lower than the former? As described in your MRI report in the first page, most clinicians describe back pain at the level of a specific bone ("at the level of the L5/S1 junction"). Referred back pain can and usually does refer downwards but not upwards.
It may very well be that you have 2 separate issues such as an acute muscle strain or spasm near your thoracic/lumbar junction and a chronic degenerative spinal condition causing the soreness/stiffness. However, I wouldn't worry about it at this point because your PT will help you sort out the muscle strain first probably using a combination of massage, heat, stretching and anti inflammatory topicals. If she's right in that the two symptoms are related, both should go away. If she's wrong, then she will help you sort out the second condition next.
Be diligent and patient and hopefully you'll be back on court soon!