There is a whole lot of information missing from your post.
1. Where are the store clerks when they misgender you? It may be that they cannot see your skirt, only your face.
2. If the store is busy, a store clerk may simply be too busy processing clients as quickly as possible, to take the time to notice your clothing.
3. What tone of voice do they use when uttering the word, "Sir"? If it is respectful, or simply polite, I do not see the need to get upset about it, if it is not derogatory or condescending.
4. You claim to be gender non-conforming, ie neither male nor female. Why insist on being gendered as female?
Methinks thou dost protest too much!