Written in response to something Denzel Chia wrote.
I had tried setting the priority variable to make the code I placed in the functions.php run later, but didn't seem to have an effect. The only way I could get it to work is if I set the following code within the wp-signup.php to run earlier:
add_action( 'wp_head', 'wpmu_signup_stylesheet', 8 );
Obviously, that's still undesirable as it involves altering the wp-signup.php file.
So, I went back to setting the CSS elements I wanted to override in wp-signup.php to !important.
I guess I just thought the wp-signup.php seemed a bit sloppy (hard-coding CSS). Seems like the options for single site registrations are more flexible. But then again, there are different beasts.