How to stop the audio pop upon reboot ?

Maybe it will help if you disable "Keep audio device alive" and "Send low volume noise" in Settings -> System -> Audio

(If you can't find it look here

Settings/System/Audio - Official Kodi Wiki

at Point 1.9 and 1.10)

I don't think it's possible without using another audio interface (e.g. hdmi, I2S, usb).

You get such pops on nearly all PC's with analog audio. I think you need additional hardware to solve this.

Add a DAC Hat.

There's one easy Solution:

Turn your Speakers off before rebooting/shutting down your RPi 3B+ !