iTerm doesn't make a bootstrap script easy, but it's still possible. I do it.

Use this to command to set the location of the iterm config folder:

   defaults write com.googlecode.iterm2 PrefsCustomFolder -string "/path/to/iterm config folder"

Then as long as that folder exists and contains your preferred settings, when iTerm opens up it'll be exactly like you want it. (though it would have been nice if this just defaulted to $HOME/.config/iTerm)