A crucial difference between Sefer Devarim and Sefer Shemot is the mention of the wooden ark that was created for the second tablets in Sefer Devarim. The explanation for this has to do with the “immanent” nature of Sefer Shemot against the “transcendental” nature of Sefer Devarim. This explains why the Mishkan and Ohel Moed are not mentioned in Sefer Devarim - because the main goal of the covenant in Devarim is the keeping of the mitzvot, and not the dwelling of the Divine Presence as it is in Sefer Shemot. 

Courtesy of the Virtual Beit Midrash, Yeshivat Har Etzion