After asking "why-did-the-mizbeach-grow-40-times", I realized (thanks JoelK) that both measurements were dictated by G-d (it's unclear to whom: Moses, David or other prophets). See also Yalkut Shimoni 1081 (thanks Meir).
Both the Mishkan and the Temple served the same purpose, but the Temples' dimensions were significantly bigger on practically everything. As the population varied greatly I assume that populational fluctuations can't count for those differences, already given by G-d.
What is the reason those two holy dwellings were so different in dimensions? Do the variations hint on changes in G-d's manifestations, or some spiritual representations?