Can I use WP comments for custom tables?

You could create a hidden dummy post and use always its post ID as comment_post_ID. Then use a comment meta field to store the related ID from your custom table.

The other, and probably better option: use custom post types, not tables if you need something that acts like a post. Register that post type with …

'supports' => array(
    'comments',
),

… and the problem will not exist anymore.

To add custom data, hook into wp_insert_comment:

add_action( 'wp_insert_comment', 'prefix_comment_meta', 10, 2 );

function prefix_comment_meta( $id, $comment )
{
    // evaluate POST request and create comment meta
}