If the damaged throw-out bearing was preventing smooth engagement / disengagement of the clutch, it certainly could have contributed to the damage to the friction surfaces.
In any case, it doesn't matter since Toyota warranty seems to consider the entire clutch assembly including the throw-out bearing as wear items. 54k is an early death for a sensibly-driven clutch, but it's not unheard-of.
Also, I am assuming the clutch items in this car are Subaru, and subary is known for AWD and terribly weak clutch hardware - especially the throw out bearings. In case your bearing has messed up the transmission snout, there are companies that make a replacement steel sleeve that slides over the scored up snout. They're not free, but it's cheaper and easier than replacing the transmission housing.
-Justin
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