I have been able to customise a flag without using Ukelele.
I have just extracted all the flags icns with this script : github.com/phible/scripts
Then, locate the icns in the AppleKeyboardLayouts-L.dat file comparing with the beginning and the end of the hexa code of the .icns, delete the code and replace it with the one of my customised icns. Log out of user session, log back in, done 😉
Here is the result with my black theme :
I highly recommend to use Icon Composer 2x to create the new .ICNS before integrating it into the .DAT. See here.
WARNING : DO NOT EVER DELETE THE .DAT IN THE KEYBOARD BUNDLE, ALWAYS OVERWRITE IT, OTHERWISE YOU KEYBOARD WILL BE STUCK AND YOU WONT BE ABLE TO DO ANYTHING !
(ALWAYS KEEP A BOOTABLE MAC OS X INSTALLER IN SENSITIVE CASES LIKE THIS TO REPAIR THINGS REINSTALLING MAC OS X ENTIRELY OR JUST FIX IT WITH TERMINAL)