The display toggle settings for the following elements does not get saved as part of the export code
User pictures in posts
User pictures in comments
User verification status in comments
When you then install the theme on another site, or revert the theme settings to the code defaults in an existing site, the display settings for all of those elements get lost, and revert to being set to display=true. This means that, for example, if you are working on a theme locally, and then then you export all of the theme settings to code, and go to your live site and revert to suck in all of your changes, things like logos and navigation suddenly start to disaply where they had previously not been doing so. The result is an incredibly broken looking theme with 2 sets of menus and logos (I'm using the logos and menu blocks provided by delta_blocks rather than the theme variable based ones.
My guess is that it's because these settings arte provided by the core, and not by the theme - but even so, if that were the case, why should revering a themes settings back to those defined in code then also revert the display settings for theses elements?