Actually, they can be pronounced the same in Chinese, too -- as a noun (meaning "storehouse"), 藏 is pronounced zàng, the same as 臟.

Oh, hah... I just checked Wiktionary to get the pinyin, and under the noun form of 藏 (zàng) it actually says "Original form of 臟／脏 (zàng, “internal organs”)." So I guess technically you could say "內藏=organs" is archaic rather than wrong. XD