Okay, so I went back to the photos I took yesterday and couldn't help notice that the Asus AIO cooler has 2 sets of 3-pin wiring. There is no 4th pin wiring on the cooler itself as per the photo here (once more):

So one of those 3-pins is wired to the AIO PUMP port. While the other 3-pin is wired by extension to a 4-pin port labelled COOLER LED by the front panel as seen here (once more):

And here's the 3-pin wiring terminating from the AIO cooler before it connectes to the supposed 4-pin RGB extension cable:

How can that be the case? So what if the supplied Asus AIO cooler is actually an ARGB and not an RGB wiring? Which means Asus themselves practically fudged the installation and probably the electronics of the LED in the cooler itself. As RGB are 12V and ARGB are 5V.
Since at this point it's probably a goner with the over voltage they have done, there's no harm re-routing the 3-pin wiring from the AIO cooler to an ARGB port in the motherboard itself. Which I did seen here:

The results? Viola!

The catch? The AIO cooler lights up on PC boot up and boot down. Then it fades back to no lights.
I removed the Armoury Crate, reboot. Same behaviour. Re-installed Armoury Crate, same behaviour. LEDs light up on power up and power down, but none while in use.
Strange.
While I did not completely solve the lighting issue for the cooler, I'm led (pun intended) to believe these shouldn't be wired to the 4-pin RGB port but to the 3-pin ARGB port. And this probably messed up how the BIOS is reading into the cooler?
I still believe it's a software glitch that won't be corrected by Asus at this point since it's an EOL unit with the arrival of new chipsets.
Thoughts? Perhaps removing Armoury Crate and just using Aura will bring better results? I'll try again tomorrow as its actually my son's PC which I bought to replace his aged G20CB.