I'd rather not have to manually re-do all the settings for all my addons in-game unless it's absolutely necessary (since I don't have memorized what the exact settings are I use, so I'd have to take screenshots of them all and then remake the settings to match the screenshots). So I'd rather get some more input about this problem before I try troubleshooting it that way.
No he's just not paying attention. The wanted quests are built into both the leveling guides and the "Zandalar Forever" achievement guide. They aren't in the rep guide because they are not repeatable and by the time you hit max level they should be done. You'll also notice the rep guide doesn't contain every single possible completable quest that rewards rep. It is designed to focus on repeatable objectives, world quests, large quest lines, and missions.