I didn't see this issue anywhere else so sorry if this is a duplicate or by design.
When I go to export a page variant that's been disabled via the UI
$handler->disabled = FALSE; /* Edit this to true to make a default page disabled initially */
is nonetheless always set.
While manually editing the export is possible as the comment suggests by far my most common use case is exporting with Features. I could manually update the features too, but ultimately a "drush features-update" would re-export the variant with "disabled = FALSE".