Religious Foods are Compliant - in the Right Context
Yes, religious foods are okay while you're doing the Whole Life Challenge. If what you are eating is part of the traditional observation of a religious holiday, then don't take away a point for what you are consuming. It's not "food" in the normal sense of your nutrition; it is more of a symbol of your beliefs and/or practice.
So, there is no penalty for matzoh during Seder, communion wafers, Ramadan feasts, etc. That said, while it’s okay to eat these foods as part of your religious practice, make sure you "eat the matzoh, but not ALL the matzoh." Your consumption should be in line with observing the holiday, but not verge into the gratuitous.