Yet, if you look at the same moves from "Enpi" which is the Shotokan version, it isn't obvious. The moves are similiar, but instead of the entry and throw it has a jumping spinning move that would NOT translate to a throw by looking at the moves. Here is a version of Enpi from a 10th Dan master of Shotokan, the throw should occur at about 1:33 seconds
Now look at an older version from Okinawa from Chotoku Kyan's lineage, throw occurs around 35 seconds
Funakoshi performing Empi kata, throw occurs around 35 seconds
Applications may have been known, but you had Itosu who made changes to the kata to make them more widespread, and then you had Funakoshi make further changes to make it even more widespread. So many moves became obscured and ridiculous applications were made up to explain them.