It was sheer stupidity just to show a flashy scene.
I just assumed it was an inverted building built by those who intended to unearth the algorithm at that location. Now that you mention it, it would pose a bit of a paradox. It could have to have been built in the future, with inverted materials, and then fallen apart shortly thereafter (due to red team). It would then have briefly recombined before falling apart again due to the blue team. It would only have existed as a whole building for the briefest of instances in the middle, and also at the very start. That logic would actually have worked for both linear and inverted timelines. As we don't see the site before or after the skirmish, we don't know what it existed as, so we can't know if it's actually an inverted building. However, I don't think it creates a problem for the time flow. I think it's just one of those unanswerable questions. It made for a cool scene too, which is nice.
In the end, it's not very important to answer the question of how the building existed, it just does. Does the future see the Freeport as a destroyed terminal building, or as a reconstructed one? We have the fortune of seeing that building before the events that destroyed it, so we know the answer to that question, but we don't know how the building appears to the people in the future. We don't know the events after that scene. I don't think it's an important question to answer either. The Freeport just exists. I think the buildings at the nuke site fall into the same category. It doesn't matter when they first came into existence, they just do. They're just ornaments on a fancy set piece. Ironically, I feel like a movie that forces you to think has resulted in a lot of people overthinking things.
It's my impression that much of the backlash against the movie is that it's not easy for most people to understand, despite all the exposition dumps. Much like the protagonist, the viewer has a hard time thinking in a non-linear manner, and the movie continuously coaxes us to break out of that mentality, as it also coaxes the protagonist. While the movie is all a predetermined loop, that loop still contains all the tension and uncertainty of your typical movie. We know with a certain level of certainty that the good guy will always prevail, and it's more about the journey to that result being entertaining. Most movies are really formulaic, and you can anticipate the end result pretty early, as well as the mechanisms for getting there. I felt no such thing with Tenet. I was certain the good guys would win, but I was never really sure how they could arrive there, until pretty close to the end, and that was due to the flow of time being so screwy. For that reason, I really enjoyed the film.
The reviewers that seem to enjoy the film the most, are those who've gone to extensive lengths to break down the linear and inverted timelines for each character. I marvel at the overall coherence Nolan was able to maintain with the story. It's really good IMO.