You get worse results in Manual mode sometimes because you have set the CPU power limits too high; the CPU is eating into the power budget of the GPU. In Black Flag for example, you can severely limit CPU power and your framerate will still be higher, because the game runs primarily on GPU power. This is a power allocation issue, not a thermal throttling issue as you have described
The 2026 ROG Zephyrus G16 is equipped with a more powerful version of the RTX 5080 and Asus even allows a maximum TGP of 160 Watts in manual mode. However, this setting is too demanding for the cooling solution and the actual gaming performance actually drops a bit.