Kafkaesqui recommended a workaround for a similar issue that may help (set /index.php?p=%post_id% as your structure permalink which will then include index.php in the comments link).
For me, this works for comments but also changes the structure of my categories and archives links to include “/ index.php?p=” as well, which doesn’t work. For example, without this workaround permalink, my monthly archives default is https://grendelsweb.com/?m=200501 — which doesn’t work. https://grendelsweb.com/index.php?m=200501 and https://grendelsweb.com/index.php?cat=5 would work, but I can’t figure out how to get that index.php in those links. The workaround fix creates an archive link of https://grendelsweb.com/index.php?p=date/ … and doesn’t work at all either (same issue with categories). If you do find where to force “index.php” into the default links calling for comments, archives, categories, or the relevant “how to” in the codex, please post. I’m sure there’s something simple I’ve neglected to do, but can’t get at it. Thanks very much!