3 pin fans have 3 wires. Hot, ground, tach. Being DC, they are controlled by the voltage on the hot, which is generally 5v low or 7v low and 12v high, depending on the fan. This sets up your duty cycle. So a 1000rpm fan with 5v low (40% duty cycle) will spin at 400rpm - 1000rpm. A 7v low (60% duty cycle) will be 600 - 1000rpm. That same fan at a 2000rpm max would be 800rom or 1200rpm lows.
4 pin fans have 4 wires. Hot, ground, tach, pwm signal. Because they are pulse modulated the hot wire will always supply a full 12vDC. This means that the fan can go much lower duty cycle since it's getting 12v. Generally you'll see lows as low as @ 20%. The pulse is like Morse code, literally tells the fan motor off/on. Fans don't instantly spin at maximum speeds, it takes a second while they wind up, so if during that windup, pulse says off, it stops voltage to the fan motor. Which starts to slow. Then pulse says on, starts to wind up again etc. This has the effect of making that fan always in a state of trying to reach full speed, but never gets there. The timing and length of on/off pulses is what sets the rpm of the fan ± a few.
The motherboard header has 4 pins. Hot, ground, tach, pwm. For a DC fan, means just using the first 3 pins, and the connector/header are keyed, so will only fit the first 3. By putting the bios on DC mode, you tell the header it has to regulate voltages and can ignore making a pwm signal. If you put the bios on pwm mode, it tells the header to supply constant 12vDC and use the pwm pin.
With AIO's, you can set the bios either way. Doesn't affect the pump, since the cpu_fan header is seperate, it's dedicated pwm. Pumps are 3 wire so will always get a constant 12v from a 4 pin cpu_fan header.
As far as duty cycle goes, that relies on the fan. A 7v low Arctic at 1000rpm max is going to see 600-1000rpm ±, whereas a 5v low generic case fan with a 2000rpm max will see 500-2000rpm ±. If you set both to 70% duty cycle, the Arctic will be at 700rpm, the generic at 1400rpm. Considerably different speeds and volume output.