Tendinitis in itself can be very persistent and very painful. There is only one cure for it, rest. Which he should be doing at this time of year anyway. Really he would've benefited from a fall shut down to let him come back strong for spring and next summer.
A PT is not qualified to opine as to a labrum tear. So I would not let what a PT speculated about get me too tied up in knots. That being said, if the PT really thought your son had a labrum tear 6 months ago, he should've sent you to an orthopedist specializing in sports throwing injuries right then and there. And if he really thought there was a possible tear, telling your son to continue throwing rates as positively moronic. So I'm wondering if he was just listing possibilities 6 months ago and not really saying your son had a tear at that time.
The problem with labrums is that even with an MRI you can never really be sure without surgery, but you don't want to have the surgery (which is pretty intrusive itself) unless you're pretty sure it's needed. Some minor labrum tears can be bolstered with a conditioning regimen, others go so far that surgery is needed. Some inflammation signatures that look like labrum tears on an MRI are really just inflammation and not tears at all. You really need to see not just any orthopaedist, but one who has a depth of experience with throwing injuries. Interpreting an MRI is more of an art than a science.
FWIW the symptoms you describe sound more like severe tendinitis to me than a labrum issue. But I'm not a doctor, either. It's time to see the right people to assure that your son is doing the right things for himself and to give yourself a chance to get on a corrective course so that you can AVOID surgery if possible.
What I would guess happened is that your ortho put your son through some range of motion diagnostics and he heard some "crunching" or similar noise that can accompany a labrum tear. The key there is that while it is indicative of a tear it is not definitive and you may merely be dealing with an impingement or even just severe inflammation from laxity in the capsule, tendinitis or some combination. While all of these are serious and need attention, a lot of these situations call for nothing more than a break from throwing and dedication to a prescribed rehab and conditioning program.
So don't hit the panic button just yet, but do stop all throwing until someone who has the kind of resume you can have confidence in is doing the talking.