OK. I have figured it out and tested.
1. Testing a domain with UA override on
Getting mobile site
2. Putting the preference to "false"
→ adb pull /system/b2g/defaults/pref/user.js b2g-user.js
51 KB/s (1859 bytes in 0.035s)
→ grep useragent.updates.enabled b2g-user.js
→ echo 'pref("general.useragent.updates.enabled", false);' >> b2g-user.js
→ adb shell mount -o rw,remount /system
→ adb push b2g-user.js /system/b2g/defaults/pref/user.js
137 KB/s (1909 bytes in 0.013s)
→ adb shell mount -o ro,remount /system
→ adb shell stop b2g && adb shell start b2g
3. Testing the same domain after erasing cookies.
Getting the desktop site.
I will update the script mozua.sh to take into consideration b2g 1.2+
https://github.com/karlcow/webcompat/blob/master/moz/mozua.sh
(be my guest with a pull request :) )