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Actually, "the mud" is simply in a different form in HF, as in: the shadow.
The corruption of Angra Manyu basically is even more stronger due to Sakura's state being much closer to full assimilation in HF compared to the other routes.
The mud itself is the very essence of the content of the grail, aka all evil of the world. Therefore, it is an inherent part of the grail/great grail, and by extention within Sakura when she is in her dark form.
This is even more evident when Shirou uses Rule Breaker to cut the "contract" between her and Avenger: she is literally purged from that... "thing", instead of simply reverting to her "normal colors". Her body was basically engulfed and corroded by the shadow, which is the essence of the grail.
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