At @milo’s suggestion, I used the post_type_link example and adapted it to my needs. This made it so only my chosen post type would be relative, while leaving any other custom post types functioning as usual.
function make_yourposttype_relative ( $url, $post ) {
if ( 'yourposttype' == get_post_type( $post ) ) {
add_filter( 'post_type_link', 'wp_make_link_relative' ); // Custom post type link
add_filter( 'post_type_archive_link', 'wp_make_link_relative' ); // Post type archive link
}
return $url;
}
add_filter( 'post_type_link', 'make_yourposttype_relative', 10, 2 );