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Terrain goes down, then objectives.
After that, you place armies (along with purchased fortifications).
You can't place an objective inside a building, but can you place a fortification on top of an objective?

Objectives get moved to top of buildings, instead of in them.
Fortifications you bought need to be put in your deployment zone.

So if someone had an objective in their depolyment zone, and then placed a Fortification on it, I would put the objective on top of the fortification.

Although, I could see the argument that the fortification couldn't be put there due to the objective already being there, but I don't think the situation is covered in RAW.

7th edition is a lot more relaxed about how terrain is placed.
I wouldn't have any particular issue with it sitting on a fortification, since it makes more sense that something valuable would be on the objective instead of inches in front or behind it.