There are many levels to the pnimiyus of a mitzvah. But we’re referring to the simple meaning behind a mitzvah that the Ribbono shel Olam writes explicitly in the Torah—as this is what He wants us to think about this as we execute the mitzvah: “I took you out of Mitzrayim, and I saved your soul. Now you have been instilled with incredible kochos because you’re no longer under the kelipah. Even right now, you have the power of freedom! When you carry out these practical mitzvos, I want you to think about the depth behind these mitzvos.”
Indeed, having in mind the reason for a mitzvah isn’t me’akev by most mitzvos. The Bach tells us that only regarding three mitzvos is the kavannah of the reason me’akev; because the Torah tells us they are in order that you should remember (tzitzis) or in order than you should know (Sukkah). And thus, one is obligated to know the reason for the mitzvah.
However, when a Yid thinks about the reason for a mitzvah and the meaning behind it, he attains an incredible connection to the Ribbono shel Olam: The Ribbono shel Olam commanded me to do this, and I am now carrying out His command. If one doesn’t do so, he hinders his growth in the kirvas Elokim that he could attain through Torah and mitzvos. The more we insist on thought and meditation in mitzvos, the closer we will thereby become to the Aibishter.