This question is dealt with explicitly in the talk by the Lubavitcher Rebbe published in the kuntress titled, B'Inyan Mikdash Me'at Zeh Beit Rabbeinu she'b'Bavel on the 28th of MarCheshvan 5752, page 419. See note 38 for details.
The essence of this is that the roof mentioned in the midrash is referring to the area that is not Kodesh and thus alludes to the Temple outside of Israel. This is the synagogue of the leader of generation.
The distinction of the people Israel, like is discussed at length in the kuntress, is also the distinction of the leader of that generation, who is Moshiach.
Like Moshe, the most distinguishing characteristic of Moshiach is his level of humility. This humility is the primary quality of the Jewish King. That in spite of being head and shoulders above everyone in the nation, he is completely subservient to his subjects in preserving and protecting their well being.
And since the Nasi (the leader of the generation) is equated with the whole generation, he actually demonstrates their defining quality too.
This last idea is one of the inner meanings behind the wording of the prayer said on the three Festivals after reciting the 13 attributes of Mercy before bringing out the Sefer Torah. That G-d should "fulfill in us the text that His Spirit should rest upon him..." is a reference from Navi to Moshiach specifically.
To appreciate this fully, the entire talk should be studied carefully including all the sources referenced.