Ok, I've had a look at the manuals for each. If the AiO's manual is to be believed the pump is a three pin connector, correct? Furthermore, it looks like the fan has a 4 pin connector on it, correct?
If this is correct, I think this is what is happening. ASUS says that it auto detects the type of fans plugged into the CPU and CPU_OPT. However since your pump is controlled DC and the fan is controlled PWM, I think the BIOS is not setting it up correctly. I think to correct this, the easiest thing to do is go into the BIOS, go into Monitor. Find the setting CPU Q-Fan control and select DC Mode. This should control the pump and the fans. Even though the fans are PWM, they can be controlled with DC Mode, they just won't be able to spin at as slow a speed as they could under PWM Mode. Also set your CPU Fan Speed Lower Limit to 600. There is also a CPU Fan Profile, it will be set to Standard. You could leave this for now and see if the above changes help. Later you can tune it with Manual and create your own profile, or you could pick a predefined one. If however you find you are still in the same situation, then you should set it to Turbo.
Do you have Ai Suite installed? This could also be interfering with the fan operation as there are fan profiles there that will override what is in the BIOS.