If 纸巾 means "paper towel", I can understand how it was combined with "face" 面 to mean "tissue". But I'm curious as to why it's 面巾纸, not 面纸巾. I can't find any definition for 巾纸 on its own, so where did this word come from?
面巾 is also a kind of napkin. 面巾 is for face cleaning, 手巾 is for hand cleaning. So 面巾纸 is usually the small pack soft paper napkin you put in your pocket, used for cleaning face. you can think it is the same thing as 纸巾. Here are many things that have different names.
This case, it is a combination of 面巾 + 纸. 纸+面巾 is also used. Though 面+纸巾 and other combinations are also logical, but less people use them.