This is strange. If you upload your metadata (see this) and let me know the upload id, I can take a closer look.
If you must clone a site running on MySQL 8+ to servers running earlier MySQL versions, you should restore WordPress’s default keys before doing the clone. Could that be part of your problem?
It has to be said, database tables don’t, for no reason, “lose their primary keys” as the wp-staging article claims. Some software, or some person, damaged your table by copying it incorrectly.
If this were my staging site with this problem, I would completely wipe it and replace it with a new clone of my production site. The point of a staging site is to have something you can test and then confidently clone to production. I wouldn’t dare clone a site with a damaged table to production.