Story mode does follow Sacchin's Normal, it was said by Nasu (somewhere). If you want to be specific, never is actually said that Shiki and Arc are lovers (Sion says it, and Shiki blushes, but doesn't agree (though neither disagrees)), nor that Shiki killed Satsuki (only that he lost her). It could happen that Satsuki became vampire, all her route happens and at the end she vanishes from Shiki's life (though she must have remained in Misaki, since she appears in ReACT). This is Normal end, after all; it won't be very happy.
"I am the spider that set this web.
-Welcome to this wonderful killing chamber."