That's something I've been wondering as well. I have a GL504GV (i7-8750H/RTX 2060) and when I tried messing around with undervolts a few months ago, I had the same behaviour - starting armoury crate would mess with XTU/Throttlestop settings (tried both), and vice versa. I've also noticed that changing the fan preset in Armoury Crate (Silent/Balanced/Turbo etc.) changes the power limit of the CPU.
I haven't found a good answer to this question, and at this point I think the only way would be to either permanently disable armoury crate (which might cause issues with RBG and Asus drivers) or for Asus to add the ability to customize voltages and power limits inside Armoury Crate itself.
Main machine: Asus ROG Zephyrus G15 GA503QR - Ryzen 9 5900HS, 16GB DDR4-3200, RTX 3070
Server: Fractal Design Node 804 - Asus TUF B550M-PLUS, Ryzen 9 3900X, 48GB DDR4-3000, Radeon HD 5670, 6TB storage
Old machines: Asus ROG Strix Hero II GL504GV - i7-8750H, RTX 2060; Asus ROG G750JM - i7-4700HQ, GTX 860m.