Sakura's presence in the latter half of "The backside of Kibisis" is actually herself intruding on Shirou and Rider's shared dream.
The finale of the main storyline states that it wouldn't be odd for her to cast a spell or two, but she's never shown using magic in any of her other scenes. This is when that happens. Remotely detecting what Rider was up to, or possibly Shirou's reversal of it, she involved herself and expressed her own feelings about her relationship with the two of them.
