The mental leaps are usually estimated from the original due date. My app for The Wonder Weeks has you put in the due date not actual birth date with an explanation of why.
Not sure about growth spurts, but wonder weeks go by EDD. My LO was 15 days late, so it's a big difference for us too! He's hit his growth spurts early too, but I think those are more flexible anyway.
Re: Growth spurt/wonder week timing question