That is the reason why everything is not solely left to the discretion of fitrah. At first, we don’t do that for cleanliness only, we do it because it is our religion. But when you look at the rationale behind it, it is none other than tazkiya/purity. There will always be some inconsistency on application of some rulings related to fitrah also, that is why I think, that some of these have been explicitly made a part of religion. Usually when something deviates from fitrah, it itself takes the form of a tradition or becomes a norm at times; but when you point towards its deviated nature, most of the times people agree with you about the rationale behind all these cleanliness measures.