Random thought the second: Bruce complaining about Clark not training Jon more intensively isn't Bruce being a pragmatic emotionless bastard, it's Bruce being emotional and rather irrational when it comes to kids. Objectively, you have to train the hell out of a Robin if you want them to be relatively safe (you can also not make or let them be Robin, but that sanity ship sailed long ago), but Jon seems to have Superman-level powers. You can always have more and better training, but when it comes to that kind of power, the main strategic concern isn't how technically good they are, but how ethically. Bruce's main concern shouldn't be Clark teaching Jon to better control his powers (which, yes, it's important to avoid accidents of he "oops, sorry about that skyscraper" kind, but it's not as if Clark isn't or won't) but rather Clark raising Jon in that very rare Clark Kentian ethical stance that made it possible for somebody with his level of power to wield it not just selflessly, but also with a politically and culturally light touch. And *that* requires Clark and Jon spending time together bonding, not training.
Perhaps seeing a child that seems unavoidably going to pick up their line of work activates Bruce's panic "must train!" fear reflexes. Or perhaps, and this doesn't exclude the previous option, training is the only way Bruce can truly conceptualize how a father-son relationship can work.
I wouldn't heed his advice, nor give him a pass on his serious and willful errors as a parental figure, but I'm not without empathy for his issues. He probably can't access his own memories of his childhood without triggering his trauma, so, as kind as he is with children (and any well-written Batman is 100% a softy and not at all scary to any kid), being a father is more of a long-term relationship, and he's not particularly knowledgeable at the not-cape bits of it.