There is a low cost option open to you to avoid the default behavior.

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

I have to disagree, because there are many implicit references happening.

E.g. reusing code from a former poster which are relevant when reading longer threads.

This becomes more apparent when trying to read complex archived threads, where one didn't follow in real-time and that context is lost.

The "simplest" solution would be to have an immediate toggle between different sort orders, in JS or as a server request.

update

FWIW: My setting is sort by reputation tho, because this has still more benefits for me.

Cheers Rolf
_{(addicted to the Perl Programming Language :)
Wikisyntax for the Monastery}