The mishna gives a procedure for adding on to the mikdash and yerushalayim. The gemara 15a learns from Ezrah and Nechemia that the process should include the 2 chometz breads of the korban Todah. Had this been necessary only during the return from the galus by the 2nd Beis Hamikdash, it would be fine to learn from Ezra and Nechemia. But, the maharatz chiyus asks that since this is a halacha for later generations, how can it be learned from Ezra and Nechemia? Futhermore, since there is a special halacha that the inner one is eaten and the outer one burned, which is not the halacha by a standard Todah, how can we learn from Ezra something which contradicts the torah? The Rashash 16a raises the same question when the gemara concludes that the source for eating one and burning is only sourced in prophesy of chagai, zecharia and mal'achi - how can we learn from there a halacha for future generations?
The Rashash is medayek from the rambam who says that one is burned and the other is eaten, without identifying which is which - that it must be a halacha l'moshe misinai that one is burned and one is eaten. The detail of the inner one being eaten and outer one burned was a temporary halacha that was introduced through ne'vuah during the time of Ezrah, and therefore not codified by the Rambam for future generations.