For so many reasons:
1. its not illegal in Japan. It is also a lot more common them people seem to think, and assumably higher than any admittance that such things happen.
2. its the same phrasing for first/second/third cousins and shares a similar kanji with a type of Close family friend. I.E. a non relative older person can be the same word as aunt or uncle to show a closeness and trust more than just a friend. This applies to Cousin terminology between kids who have no blood relation but are raised together as if they are family.
3. It can serve as an easy motivator or internal conflict for the person feeling the crush. "I know I shouldn't" But feelings happen they aren't chosen. Lets the character have reasons to "hate" themselves.
Pretty sure the two FMC's are intended to be the final couple... seems pretty obvious to me. Can 100% assure you its not going to be central to much of anything outside of its part of Fujimi Shouko's past.

Why tf is there sm incest in yuri, like if i had a nickel everytime, i could retire comfortably...
But still the main characters are super cute. That subplot will hopefully fade away soon