Thanks for the reply. I think I just realized I was confused and should have been asking a different question. If I disable comments manually, instead of a link to the popup it just says "comments closed," but if I allow WP to automatically close comments, the link remains for the popup and the popup still shows previous comments. So that's ok. I'm guessing there's a difference between "disabling" and "closing," so that was my misunderstanding.
But, a related question: When WP automatically closes for me, if users click on the popup link, the popup appears with a comments form and only tells users that comments are closed after they've tried to post the comment. Is there a way to put a notice right in the popup instead, so they don't go to the trouble?
Also, on my single page, I am using the comments template (not the popup), and there I can see the previous comments, no form, but there is nothing stating that comments have been closed. I copied both files from the default, so I'm not sure why the inconsistency. Any ideas?
Thanks again.