I would change it to paginated from infinite scroll.
"This suggestion lacks a reasoning behind it"
It would be an easier way to navigate through the comments. Say there are 20 "pages" worth of comments and you know you've read up to page 12, you could instantly load up page 12 instead of going through the other pages. It's more user friendly and it would reduce the load on the backend trying to retrieve comments the user isn't interested in anyway.
If you would allow links/references to comments, it would be easier to navigate up and down the comment to read the context and responses. This would synergize with panzer's other suggestion of "multi-replies", which is essentially allowing a single comment to refer to multiple other comments. E.g. how BBCode would have a linkable quote tag or whatever it is that 4chan apparently does:
panzerkampfwagyu said:
Maybe they could make it so, that if multiple comments are answered to, the tree instances the comment below all three, while adding references to the post numbers that preview and move the page to the selected post, similar to how 4chan does it.
The current comments flyout doesn't feel particularly nice to read a lot of comments in. It's a very limited space and once people start posting long-form essays in there, it will definitely be rough to go through in that amount of space. Most sites with infinite scroll in their comments section would typically have some kind of most relevant/highest rated ordering to give the user a better selection of comments right off the bat, expecting the user not to go through all the comments. This is why those sites can get away with infinite scroll and restricting comments to fit in a tree-structure; because the ordering will change over time.
I personally don't like that, since I usually read all the comments if I'm interested in reading them for a particular chapter. I do come back to some of them multiple times, especially if I've either uploaded the chapter or posted a comment myself. And that's harder to do if the ordering of comments would change.
If MangaDex is not going to implement a similar system where the ordering of comments could/would change, then pagination would make more sense, due to the reasons given in the first paragraph and potentially the second paragraph.