Are the Shafa and Witr prayers two separate prayers, or are they one prayer (Witr) that can be performed with three or five rak’ahs? And if someone prays Witr with a single rak’ah due to lack of time, should they make up the Shafa after sunrise?

The Shafa prayer alone is not to be made up by someone who prayed the Witr as a single rak'ah, because the Shafa is linked to the Witr. The Witr is the prayer with which one concludes the night prayer, and it is called such because it is prayed as an odd number (one rak'ah or three). If a salutation separates the last rak'ah from the one before it, then Witr is the name for the single, separated rak'ah, and what preceded it is Shafa. As for someone who missed their regular night prayer, it is legislated for them to make it up after Fajr.