Yes. Pi 3 and Pi zero both comes with two hardware timers (PWMs). I have detailed how to enable it here:
https://learn.adafruit.com/reef-pi-installation-and-configuration/raspberry-pi-configuration
After you have configured it, you can declare jacks (PWM connectors) in reef-pi to use those two pins by slecting driver as "rpi" (other option is to use PCA9685), and pin number 0 (for GPIO 18) or 1 (for GPIO 19). Rember, Pi's pwm are 3.3V , unlike PCA9685 which is 5V. But this should not make any difference in most cases (since we use NPN transistor or meanwell drivers to convert that Pi/PCA9685 pwm to 10V or something else suitable for the LED lights, and both NPN transistor or meanwell drivers work on 3.3V pwm just fine)
let me know if you have any more questions