I am adamantly, absolutely ironclad against a comment voting system. A huge part of this community's relative civility (unless
@Zephyrus is suddenly getting a lot more reports recently - are you?) is that there is as yet no easy method of forming tribes and the resulting internecine cold war that plagues so many other sites. If you want to find people who agree or disagree with you, there is no option to do so except hunting them down yourself.
Y'know, Batoto had an upvote-only system for comments ("likes", not anonymous) and was roughly the same civility level as Mangadex, heck possibly slightly more civil on average (though I wouldn't attribute that to this, of course; see my final paragraphs).
Between that and just my gut feeling based on my own experiences with such systems, I'm semi-convinced that downvotes are really what make things toxic: With upvotes you can see who's winning in popular opinion, but in general it doesn't have the same flame-fanning effects as the "you suck" (downvote) button. Which makes intuitive sense—with a bunch of downvotes one feels the need to defend oneself against attack, whereas with just a lack-of-likes, one usually just feels a bit, well, ignored.
Having said that—the first difference between different sites' civility is usually the
people on the site. Webtoons.com, as an example, has the upvote-and-downvote system but the site is full of friendly/touchy-feely/open-minded sorts and pretty much the only way to get downvote-bombed is to be sexist, racist, or homophobic (or just mean). Seeing a comment with any downvotes is rare. That's just a byproduct of the audience the site attracts, but, the audience a site attracts is affected by the community it has so this gets recursive quickly.
This site imported a bunch of Batoto's population so it has a good start; Batotonians were pretty civil on average by internet standards. Beyond that, it's pretty much up to the mods to nudge the site population subtly in a certain direction (e.g. rules that discourage shitpost-culture) to keep the existing community from succumbing to random noise and becoming, essentially, internet-average.