Was the reason for not considering Mecca permissible to conquer in the past due to its location and Allah Almighty's protection of it?

Mecca has never been desecrated mistakenly. Rather, it was desecrated by wicked transgressors, such as the people of Al-Sham during the time of Yazid ibn Mu'awiyah, and the Qarmatians who killed Muslims and removed the Black Stone. The security of the Sacred House mentioned in the texts means that security is the predominant state in Mecca, and it does not preclude the occurrence of brief and incidental periods of fear. Alternatively, the intended meaning of security could be security in terms of jurisprudential rulings, not cosmic events.