How can I set a placeholder variable in page.tpl.php from a page callback?
There are a few possibilities, not sure which one would work best for you. There isn't a really easy way to do that.

I would say the "drupal way" of doing that would be to expose your additional content as a block. You can configure that to only show up on specific pages and place it above the main content.

There is also hook_page_alter(), but that requires the same conditonal checks as a template_preprocess.

You could also return a render array in your page callback and then display it separately in your page.tpl.php, something like render($page['content']['system_main']['part_a']) and so on. You could do that only in a template suggestion for a specific page, like page--yourpath.tpl.php.

To avoid messing with page.tpl.php too much, there is also the possibility of overriding the so called 'delivery_callback' (see menu_execute_active_handler() in your menu router item for that page. The default delivery callback is drupal_deliver_html_page().