I'm not a trainer and don't know anything about the physical care of racehorses so I could only make fairly uneducated guesses but I would say it is highly likely that his physical issues have a great deal to do with his relatively light schedule. I guess when you have those concerns, especially with a supremely talented horse, you would tend to err on the side of caution.
I also agree that having Bernardini in the barn makes it easier to pass a race like the Classic. When you likely already have the favorite it certainly lessens the temptation to " take a shot " with another horse, so to speak.
One thing I will say is that in my experience even good horses tend not to perform up to their potential when they are placed, or sometimes rushed, into major races that they were originally planning on passing.
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