After looking at the User Template folder, I noticed a Non_localized.lproj folder. It seems that this folder also has a .GlobalPreferences.plist! Instead of changing the English.lproj GlobalTemplate file, I changed the Non_localized.lproj GlobalPreferences file. Bam! It worked for all new users.
My guess is that your specific language template file, such as English.lproj in my case, is being combined with the non_localized.lproj file for whatever reasons.
Here is the command I used:
sudo defaults write /System/Library/User\ Template/Non_localized/Library/Preferences/.GlobalPreferences AppleMiniaturizeOnDoubleClick -bool TRUE
That allows all new users to double click a window to minimize it. Enjoy!