I have resolved the aforementioned issues with a hotfix on the testing branch; please test when time permits. Executive summary:
The mod fully restores the DOM tree to its original state when toggled off. It is now possible to toggle the mod on and off on the same page without reloading, and changes will behave as expected.
For reasons of security, the mod no longer allows clicking the post headers or post body as a means of collapsing/expanding comments. This was attaching unnecessary listeners to elements on the page, with no way of clearing them when toggled off (besides hard refreshing). Now the only approved way of expanding/collapsing is to use the +/- icon or colored bars.
The mod erroneously modified the CSS of profile pictures to give them rounded borders, which was unspecified by its intended behavior and documented nowhere in the description. Now they conform to the standard square format.
The superfluous mores are being removed now for comments with overflow text. What I thought would be a quick fix turned into hours, and I thought I was losing my marbles over this one for a long time, since the tree clearly showed numerous duplicate mores, but only one per comment was being shown at runtime of the script. At first, I did not seriously think that the mod was completing its runtime cycle prior to the duplicate mores being spawned, but indeed this is what was happening. For now, I have added a 20ms sleep before clearing the extra mores, and this seems to suffice to let them propagate before the mod can continue with the cleanup phase. This seems satisfactory for now, short of attaching observers to wait for the duplicate mores to appear.
I believe that covers everything. It should be possible to switch the mod on and off at will now and see no adverse effect.