I messed around with the code some more, and my particular issue actually ended up relating to the original if statement parameters. Changing the condition to check the home page for queries to
if ( $query->is_home() && ! $query->is_main_query() ) {
return;
}
and
else {
//This is the first page. Just use the offset...
if ( $query->is_home() && $query->is_main_query()) {
$query->set('offset',$offset);
}
}
}
made it so that the existing offset and posts per page arguments would be true for the main query loop, with the default else conditions declared in the index.php file applying to the secondary grid loop as desired. The second if statement condition needed to be added since without it there was a weird theme breaking bug that kept removing the first six items from the media library and posts.
These links might help clear up similar issues:
https://wordpress.stackexchange.com/questions/tagged/pre-get-posts