When I was learning this vocab two years ago, Wanikani listed both readings, はやくち and はやぐち.
Then they removed はやぐち (they probably had some reasons about it being much less used or else, do not remember). What I remember is failing couple of reviews due to this 
As for rendaku script, I suspect it works of the WK content snapshot taken when the script was created, and thus later edits may not be reflected in the script. So the script still remembers rendaku’d version and says “yes rendaku is Ok”.
EDIT: it was way too easy to find the content update notice when the other reading was removed:
November 13 2020 Content Updates