Our inner self speaks and we can find the divine voice even in our ignorance. Our understanding or misunderstanding of Quranic words does not mute this voice. Any lack of understanding does not pass as an excuse. Because at the end there will be no precondition when we face our Creator.
Please note your very last sentence of your post. You said, Dr. Shabbir titled his work as “The Quran as he Understood.” While the correct title of his work is “The Quran As It Explains Itself.” Did you mean to highlight any difference here?