This is going to sound like nitpicking but is there a way that you could avoid the flicker on the listing page?

Perhaps adding the <div> on load with a static height and then filling it with the filters? Another option could be to allow the user to show / hide the bar and remember the setting. That way, one could open it when needed only and it wouldn't flicker on every load.

Same thing for the "toggle all comments" button in a thread.

I get nauseous with such flickers. I really like this extension but won't be able to use it unless this changes.