Can I specify the location of a .tpl.php while using preprocess hooks?
It has to be in either the module defining the theme function or the active theme, unless you want to make override in the theme registry.

Drupal provides a hook: hook_theme_registry_alter that allows you to alter the theme registry and thus also where Drupal would look for template files. Messing too much with this tends to make it blow up into your face, as you alter some default Drupal behaviors.