So it seems there may be a chance that some routers shipped with manufacturing mode left enabled, despite what I was told about it. Really odd.
So, what's left to do:
If you have actually replaced your bootloader, then please flash back the original bootloader (you DID keep a backup, right?), as who knows what else this custom bootloader might be breaking (I know that WAN monitoring is NOT the only thing affected by it...).
If you have a non-Asus router that you hacked and are running an illegal firmware build on it, then go away. You're on your own.
If you bought it and it truly came that way, and you are sure it wasn't refurbished or sold on the grey market after being region-modded, then the best suggestion I can make is to flash back the stock firmware (must be 384_81351 or newer), confirm that the issue still exists with stock firmware AFTER a factory default reset (Internet showing as disconnected), then ask for an RMA on the grounds of that issue. Asus should replace it/fix it under warranty.
If it's out of warranty and/or you don't want to RMA, then I don't know what else to tell you. Yes, it's possible to fix it, but it requires a procedure that is not publicly available. Any post discussing that method will be deleted, because that information can a) be used to cause MORE issues if misused, and b) can be used to break local laws by also messing with the router region, and therefore falls under the forum-wide ban on discussing such procedures.
I will evaluate my own options. I can skip that mode check so at least WAN monitoring will work normally, however I cannot guarantee that you won't also suffer from OTHER issues. So, it would just be a band-aid at best, and anything else can potentially break in the future if Asus keeps adding more checks throughout the firmware code.