The words Mishkan and Mikdash, in their general contexts, both refer to a Sanctuary dedicated to the worship of God. However, in their more specific usage, the Mishkan refers to a temporary Sanctuary (Tabernacle, a tent-like structure) whereas the Mikdash (Temple, as built by King Solomon) refers to a more permanent structure.
All commentators must agree that a permanent Sanctuary, the symbol of the nation of Israel's relationship with God, (call it Mishkan or Mikdash) is "l'chatchila" and a basic theme in Chumash. The dispute between Rashi and Ramban relates only to a more "technical" issue: the need for the nation of Israel to build a temporary Sanctuary, i.e. the Mishkan, prior to their conquest of the land of Israel.