I have completed an audit of the mod and observed the following issues:
Does not properly unset classes and restore the page to an intact state when turned off: this was having the side effect of making the threaded lines look incorrect when toggling on/off in place. The mod should not leave dangling containers around after it is toggled off. The mod creates an outer container so that the "expando" lines flow all the way down through the child elements, but when turned off, these child elements need to be moved back out of the container to be adjacent to each other and the container removed. => Fixed locally.
Does not properly unset event listeners attached to nested comments. Same as above, tends to leave dangling listeners and does not unset itself cleanly. => In progress.
Because it physically manipulates the DOM and moves sub-comments into their own container down the tree, triggers an event (likely a bug) on Kbin's side whereby any time the DOM is updated for that element, Kbin appends a more element (text expansion button) if the text overflows a certain length, even if a more element is already present. You can test this by creating a dummy div above or below a long comment and then moving the long comment before or after that div. Simply moving its position in the DOM will trigger the creation of another more element inside. And because the mod puts each comment into its own container for the purposes of threading nested chains of comments, this will trigger the creation of as many mores as there are indendation levels. So for a comment chain 5 replies deep, there will be 5 mores. This is further exacerbated when toggling the mod on and off, since these mores are not getting wiped and will just keep getting stacked up. Since this is also an upstream issue, our only alternative here is to walk through the tree and remove the extraneous more elements after nesting occurs. This is similar to your CSS solution, but instead of masking them, physically deletes them, otherwise we will have a constantly growing tree of mores every time nesting happens. I guess this should also be reported upstream as well. Kbin seems to expect no DOM manipulation to occur, which is reasonable, I suppose, but might be better if the callback doesn't insert the more element at all if it's already present. => Easy fix on the Kbin side, in progress.