Gareth, I believe that some of what Dan is seeing is the result of the changes that came with 3.11 and Activity Complete, some of these that I mentioned in my topic "Collapsed Topics Plug-in, Problem with Moodle 3.11
." In that post of mine, I let you know that I appreciate that I prefer the way that your Collapsed Topics retain the checkboxes (as in Moodle 3.10), instead of the newer "Mark as Done" buttons. Of course, I hope that your Collapsed Topics continues to do this!
What I have noticed is that when I am in "Turn editing On" mode, that these buttons still show. This is not bothersome to me at all. When I turn off edition, the older checkboxes show. In fact, this suggests to me that it might be rather simple for Collapsed Topics to have a switch for "Show checkboxes instead of mark as done" option. Of course, I am not the programmer so the effort that you, the real programmer, have to go through will always seem "simple." 😀
My guess is that Collapsed Topics either didn't have to worry about the visual effect during "editing," or that something in 3.11 has changed for both "editing" and "non-editing" modes.
I say all this to help you figure out what you might want to do in upcoming versions of CT. Let me know if you need more information. Again, thanks for all that you have done and your dedication to the excellent Collapsed Topics plugin.