Is there any way to use a different theme file for a Mediawiki's front page, while the rest of the wiki uses the standard theme you set? For example, say I use Monobook.php for all of my regular pages, but Custom.php for my wiki's front page. I can't find anything that would allow me to do this.
Sure. All you need to do is use a hook, check if the current
$wgTitle is the same as the main page title, and if it is, switch the Skin object to a different skin.
The hook you should use for this is
Skin object is passed by reference there, so you should have no trouble replacing it with a custom skin of your choice.