To answer the contradiction between the Beraisa, which rules that the roof is holy and the Mishnah, which rules that it is not, the Gemara establishes the former with regard to placing the 'two Amoh sticks' (matters concerning the building), and the latter, with regard to eating Kodshei Kodshim and Shechting Kodshim Kalim (matters that concern the Mizbe'ach).

Hence Rashi says that they are Kodesh with regard to matters concerning the building but not matters concerning the Mizbe'ach.

Be'virchas Kol Tuv

Eliezer Chrysler.