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You are portraying Bauer as hard headed and self-centered when I see no evidence of that. He may have his own routine, but that's because he is so driven to succeed that he has methodically determined the optimal approach for his skill set. If every player was like him the team would be much better. If he were stubborn and doing things without good reason, then this might a serious issue. That's not the case. His workouts would very likely conform just fine with what the M's are doing, at a minimum their heavy emphasis on long toss would be in sync. If anything, I would bet that Bauer would absolutely jump at the chance to work with Dr. Elliot. Bauer is extremely analytical and wants to know about cutting edge ideas, and Elliot seems to be interested in implementing the most modern approaches to pitching development available. They'd probably be work great together. It's the teams with backwards attitudes toward long toss that would have a problem with him.
Bauer is like Ichiro. Ichiro has his own routine that he follows religiously, but that isn't because he has a giant ego and doesn't care about the team. On the contrary, he is intensely competive and it kills him when the team struggles. To say that someone is selfish and only concerned with themselves simply because they have an unorthodox workout is absurd. If I were a manager, I'd love to have 14 Ichiros and 11 Bauers. I'd have the hardest working and most fundamentally sound team ever, and I'd win A LOT of games. And I'd probably have less clubhouse conflict than normal because everyone would be so focused on success.