It's not only zoning; it could be foundational as well: Tall skyscrapers need a sturdy base to build on, the closer to ground level the better and cheaper it is

It's not only zoning; it could be foundational as well: Tall skyscrapers need a sturdy base to build on, the closer to ground level the better and cheaper it is. In New York, it's why Manhattan has the majority of skyscrapers - bedrock is essentially just below your feet. Other places have to do things differently, which are more expensive - like driving deep piles or digging deep sub-basements to reach bedrock, or a combination of both.