He does also get pretty sheltered minutes - high o-zone faceoffs, low d-zone faceoffs, low quality of competition. This stuff does matter a lot - for example Travis Dermott always had excellent on/off-ice stats (real goal differential, expected goal differential, CORSI/Fenwick/etc.), but also got sheltered minutes, and he was ultimately a very borderline NHL dmen who never went anywhere once he left the Leafs. Starting in the o-zone against bottom 6 competition is just massively different than starting in the d-zone against top lines, it has a tremendous impact on on/off-ice stats.
I am a big Lily fan, I do think it's worth giving him more responsibility and seeing how he handles it, but you can't take on/off-ice stats at face value, without looking at how difficult the minutes are (o-zone/d-zone faceoff percentages, quality of competition). Lily has so far been seeing quite sheltered minutes, his numbers won't necessarily hold up if given tougher minutes.
Just watching him, I'd say Lily is quite a good 1-on-1 defender - good skater, solid build, hard to beat 1-on-1 unless you can catch him out of position to start. Positionally he's often good, but is more prone to getting caught in no-mans-land than our top defensive dmen, like Brodie and McCabe. On breakouts, I feel like the talent is there, and he's often good, but he does get stuck in his own sometimes, he just straight up bobbles the puck, whiffing on stick handling and passing more than any other core Leafs dman. I do think he's a quality dman overall, but he does have some holes in his game. I think they're mostly confidence related/mental, which is why I would like to see Keefe show some strong belief in him, give him tougher minutes and positive encouragement, and see how he does. But I also do think his on/off-ice stats are helped out quite a bit by fairly soft/sheltered minutes, I don't think he's better than any of Rielly, Brodie or McCabe, today, but I do think he's our 4th best dman, with plenty of upside to become better.