I've always set Xorg options by setting these on ~/.xinitrc or ~/.bashrc:
setxkbmap -option "ctrl:nocaps" xset r rate 300 50
This method meant that anytime i reconnected keyboard, or if a new one was attached, then the configuration would not apply. I had to manually run the command again. That was suboptimal.
However, after using wayland for a while, it had objectively better method: Let the composer handle that. Thus I searched for ways to do it in Xorg's config. Turns out, it's been right there since forever!
The answer was found on Arch Wiki. Now, i can just set the xorg config once, then all new keyboards i connect will always work with the same config!
One thing i didn't understand was: why was nobody writing about this? I've searched this exact question a lot of time throught the years, and all of them only mentioned setxkbmap and xset. None of the other posts mentioned "you could set it in xorg config as well". Most of them advised you to stick that on your ~/.bashrc or something similar.
The solution:
Section "InputClass"
Identifier "system-keyboard"
MatchIsKeyboard "on"
Option "XkbLayout" "us,np"
Option "XkbOptions" "ctrl:nocaps,grp:shifts_toggle"
Option "AutoRepeat" "300 60"
EndSection