Like if each edition of an ebook had its paragraphs rearranged based on how much time people spent reading them
You are mistaken. Replies to a node should not, and in general do not, depend on each other. Sometimes, of course, a later reply will say something like "As Ovid said above..." - and this can seem slightly strange if Ovid's reply is now below instead of above. But that's extremely minor.
You would have a point if replies in a thread were presented out of order, like:
Jim: comment 1
Jim: comment 3
Bob: comment 2
But we never do that.
I reckon we are the only monastery ever to have a dungeon staffed
with 16,000 zombies