BK,
I have heard that PT/trainer "you can keep playing and it won't cause further injury" information before.
Don't and I mean do not believe it unless and until you have a solid diagnosis based on the most sensitive medical testing that needs to be done.
If it can be proven the labrum is intact and you are dealing with impingement/bursitis, etc, it is a different issue in terms of playing and throwing, perhaps.
What seems a bit quizzical from your post is the location of the pain and the diagnosis of rotator cuff tendinitis. I believe you will find the pain from that condition is normally located on the back of the shoulder and especially occurs with deceleration during the throwing motion.
Our son was diagnosed with a labral tear based on a contrast MRI. Was told he could continue to play through his Milb season without causing more damage.
Our son followed the medical advice/trainer advice and played nearly an entire Milb season with a labral tear.
When the surgery was done, the assessment was there was a lot more damage than they thought. Now whether it was there and not detected on MRI or more damage occurred from following their advice and playing, well, they just "couldn't tell."
Does your son complain of any clicking in the shoulder during throwing?
Does he talk about the shoulder feeling loose or unstable during the throwing motion?
If you are getting him a second opinion, which is great I think, and going to FLA., I would urge you to consider having your son seen by James Andrews, MD.
Based on our experience, the "team doctor" stuff sounds good. It can end up being a very "hollow" sound both in terms of diagnostics and treatment.
If this were my son, knowing what I know now, I would want the very best sports doctor I can find, who is objective, a patient advocate, who knows shoulders, knows baseball players, and has a history of success in diagnosing labrum damage vs bursitis vs impingement vs some combination, who has the history of providing a plan to successfully prevent surgery, and has the best record of success in doing surgery, if it is needed.
As others have said, do your research. There is an April 2008 report from a Phillies team doctor. Shoulders are complicated. Knowing what I know now, and what our son experienced, I would not permit my son to play any baseball or do any stressful action(weight lifting) with that arm/shoulder until you and the doctors are clear on the diagnosis.
There may be doctors as good as James Andrews for shoulders. There are none better in terms of results.