This highlights where reality and authorial intent don't always jibe. Midgar was conceived as being large enough that Tokyo's 23 special wards would fit within -- but at the same time, Jesse says the plate is only 50 meters from the surface. Which is absurd.
Even a quick glance would tell you the plate is more than 164 feet high.
Coming back around to Midgar's diameter, let's say that it is just twice the height of the Shin-Ra building and go with that for a second. In the real world, our tallest building is the Burj Khalifa at 2,717 feet. Check out pictures of that and you will believe it could be the height of the Shin-Ra building.
Doubling its height, though, would give us just 5,434 feet -- only a tad past one mile. Midgar is, I would argue, obviously meant to be more than one mile across. At less than eight-tenths of a square mile (going by the "area of a circle" formula), not only is that not anywhere close to encompassing the area of
the 23 special wards, it's not even halfway sufficient to encompass
the downtown area of Charlotte, North Carolina (it would still come up significantly short on this even with a diameter of a mile and a half).
Of course, assuming the Shin-Ra building is equal to half the diameter of Midgar, in order for the area of the city to be able to absorb Tokyo's 23 wards, the diameter of Midgar would need to be 17.5 miles, requiring the Shin-Ra building be 8.75 miles tall.
I do think we can safely rule that out, particularly for a building that's only supposed to have 69 floors, but the only thing that makes "sense" is that the Shin-Ra building is still meant to be ridiculously enormous -- like at-least-a-few-miles-tall enormous.
Which ... isn't altogether out of the question, I guess? The building
does need to be big enough that the location of the Turks' secret headquarters went undiscovered for
three years while President Shinra had Scarlet searching for it.
I don't know, these game designers weren't civil engineers.