Junk mail rule marks as read messages in All Inboxes

I'm not sure why it affects all the messages, but a rule only runs automatically on message that enter the Inbox.

If you have the Junk filters enabled, there is a setting to filter junk mail before applying other rules.

If you did not do so, you might want to set Perform custom actions in Junk Settings, then click Advanced and add the mark as read action after Move to Junk folder.

Since you have the Filter junk mail before applying rules set, any Junk rule you make in Rules won't affect the messages that have been already moved to Junk by the Junk mail filter.

As I suggested, use the Advanced button to add a "mark as read" action to the default filter.