It seems to me that they are indeed the same structure, though it is interesting that some chapters of Exodus seem to prefer one term over the other, much the same way that we seem to occasionally see some chapters prefer one title for God over another. Rather than see these of necessity being an evidence for differing authors or even differing literary sources, it seems that these can be seen merely as occasional stylistic fluctuations. As you noted, both terms are heavily in evidence in chapter 40.

The Hebrew term MISHKAN is used of the Tabernacle as well as of a dwelling place in general

Psalm 26:8. O LORD, I love the habitation of Thy house, And the place where Thy glory dwells

Psalm 43:3. O send out Thy light and Thy truth, let them lead me; Let them bring me to Thy holy hill, And to Thy dwelling places.

It would seem, then, that the references to the Tent of Meeting are more specific to refer to the USE for which the Tabernacle was intended.