Did some research and found answer myself, post it here just to share with others
"Use Bold Font" is part of a dictionary, and we need to use plistbuddy to change it, here is the command to see the current settings
[admin@mb-125:~] : /usr/libexec/PlistBuddy -c 'Print :"New Bookmarks":0:"Use Bold Font"' ~/Library/Preferences/com.googlecode.iterm2.plist
true
And this is how you change it from command line
[admin@mb-125:~] : /usr/libexec/PlistBuddy -c 'Set :"New Bookmarks":0:"Use Bold Font" false' ~/Library/Preferences/com.googlecode.iterm2.plist
Check again
[admin@mb-125:~] : /usr/libexec/PlistBuddy -c 'Print :"New Bookmarks":0:"Use Bold Font"' ~/Library/Preferences/com.googlecode.iterm2.plist
false
So basically you should be able to change all the settings from command line.