The Apple touch icons (aka. Webclip or Homescreen icons) can not be changed via custom themes. This is a technical restriction of mobile Safari which does not allow runtime changes to these icons. You can provide one set of touchicons which is used no matter what theme is installed or used by the user.

For more informations, please refer to le_homescreen_icons

The .htaccess can also be used to do more advanced rewriting for special theming cases, i.e. domain-based login themes for multibrand installations