Exactly. I think it also depends on what you classify as 'passing a physical'. If Tanaka took a physical, it would tell you the ligament in his elbow was slightly torn. Would the team say "well we already knew that" and classify the physical as 'passing'?
When they say someone 'failed' a physical, I've always assumed it's that they've concluded some pre-existing condition was simply worse than originally expected and they weren't comfortable with it.
It's like a home inspection - there's always something slightly wrong, it's just a matter of how many things are wrong and whether you can live with them or not. I have to imagine most athletes have pre-existing issues. A bad back (Paxton), a bum knee (Pedroia), an ankle that didn't heal the best (J.Polanco), a separated shoulder that pops out more than normal (Bellinger), Arthritis (Flores), etc.