How do I display only the latest post on my home page, while maintaining proper plugin hooks?

I’m not sure how plugin hooks would impact in any way the solution to your problem. The home.php template file gets included at the template_redirect action, which fires well-before wp_head.

That said, what it sounds like you want to do is:

1. Have 'posts_per_page' = 1 on the first page of the blog posts index
2. Have 'posts_per_page' = 10 on subsequent pages of the blog posts index

The simplest method is probably to use a static page as the site front page, and then use a custom query in front-page.php to retrieve the latest post.

front-page.php:

get_header();

$latest_post_args = array(
    'post_per_page' = 1;
);

$latest_post = new WP_Query( $latest_post_args );

if ( $latest_post->have_posts() ) : while ( $latest_post->have-posts() ) : $latest_post->the_post();

    // Loop markup goes here

endwhile; endif;

wp_reset_postdata();

get_footer();

Since is_singular() returns true for static pages as the site front page, your plugin script enqueues should be unaffected.