As of version 0.18, generators can use gulp plugins to process file writes. This allows generators to ask a user their preferred indentation and apply it to the output.
You can see more about this technical detail on the release announcement: http://yeoman.io/blog/release-0.18.html
It is important to note that every generator is free to implement that feature. It is not something yo
will (or can) enforce on his own. So feel free to open tickets on the generators you'd like to see implementing that feature.