Well, okay, a friend helped me to find a workaround.
We edited the wp-includes/link-template.php and made a preg_replace at the point where it generates the wrong path.
function next_posts( $max_page = 0, $echo = true ) {
$output = esc_url( get_next_posts_page_link( $max_page ) );
$output = str_replace('marcbauer/wordpress/','' , $output);
It works!
Although it doesn’t solve the underlying problem of generating the wrong path in the first place. But I’m fine with this.
