Site template override not enabled when default theme and admin theme are identical

Outset

In panels_everywhere_page_build() if you just have the variable 'panels_everywhere_site_template_enabled' set to TRUE (but you don't have 'panels_everywhere_site_template_per_theme' set to TRUE) you eventually reach this code path (see here):

if (!variable_get('panels_everywhere_site_template_enabled_admin', FALSE)) {
  $admin_theme = variable_get('admin_theme', '0');
  if ($admin_theme && $admin_theme == $theme) {
    return FALSE;
  }
}

return TRUE;

(Note that this is in panels_everywhere_should_override() which is called from panels_everywhere_page_build(). TRUE then means that the override will be applied and FALSE means in won't.)
I'm assuming here that 'panels_everywhere_site_template_enabled_admin' is not set to TRUE.
If one sets the 'Admin theme' setting to 'Default theme' in the UI, the 'admin_theme' variable gets set to '0' and, accordingly, the if ($admin_theme) part returns FALSE (because (bool) '0' === FALSE). Therefore the entire code block above returns TRUE.

Problem

If one sets the 'Admin theme' to the actual default theme, then the 'admin_theme' variable gets set to the theme name, e.g. 'bartik'. In that case the entire code above returns FALSE (because (bool) 'bartik' === TRUE) and, thus, the site template is not applied.

Arguably, this is a misconfiguration, but since it is pretty hard to debug I would suggest to add an additional check so that the if () in the code block above becomes

  if ($admin_theme && $admin_theme == $theme && $admin_theme != variable_get('theme_default', 'bartik')) {

I have not marked this as a bug, though, because it is sovable very simply by simply setting the 'Admin theme' to 'Default theme' in the UI. (You have to realize that that is the problem, however...)

I will provide a patch in #1.