The most accurate bit of Clark Kent characterization I've seen in a while is Superman explaining to his son, with a calm and almost wistful expression, that he thinks about killing Batman every single day, because, God, that man can be annoying.
At some level, I think Clark appreciates Bruce developing all those kryptonite failsafes not just because mind control is an occupational hazard, but because it shows that Bruce sees him past both his "Superman" *and* "Clark Kent" personas, to the underlying Clark who, alright, *won't* punch your head into orbit because he's way past done with your shit, but by Rao does think it'd feel wonderful (there's an analogy there with the Bruce that's neither "Batman" nor "Bruce Wayne", although I'd think in terms of Bruce doing something Batman-level for non-Mission reasons, not the more psychologically fraught killing bit).
(Also: remember that bit when Clark was jealous that Bruce could get away with punching Guy Gardner, because he was sure it felt wonderful but he can't.)
Random thought the first: Why does Clark say "Rao!" as an spontaneous expression of surprise? He learned about Kryptonian culture, but as an adult, and even if we grant that Kryptonian teaching techniques might be particularly intensive, all of his habits and beliefs are compatible with his contemporary US upbringing, and don't reflect any Kryptonian influence. His religious leanings seem to be toward a vague ecumenical theism, any specifics rather questionable given his personal experiences with literal angels, gods, devils, and, let's not forget, his personal death and resurrection, which for any strongly normative Christian should've been quite disquieting on theological grounds (now there's an AU for you; a very specifically Christian Clark Kent would have had pretty much the same exact career as Superman, with the same morals and understanding of himself as an ordinary person with extraordinary abilities that give him extraordinary responsibilities, but what would personal resurrection filtered through Christian dogma do to his self-image?) And anyway Kryptonians of the Jor-El era seemed fanatical about cultural (and genetic?) "purity," not religion. So is "Rao!" an affectation? Did late-stage Kryptonians use it as an expletive, and Clark got into the habit of using it because when, say, a huge sentient space crab suddenly appears over Metropolis with the intention of impregnating the city you have to say some variant of "oh shit!" but Superman isn't supposed to?
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.