Software cannot be built like skyscrapers because the sponsors know about the malleability of the medium and treat it like a lump of clay that by adding water can be shaped to something else.
Funny you bring up the clay analogy.
It was discussed here just 2 days ago intensively.
But software is in fact not very malleable at all. It's true the medium supports change, it's just a bunch of bits, but change is actually hard and expensive, perhaps more than other mediums.
You're mixing up design and manufacturing. A skyscraper is first completely designed (on paper, cad systems, prototypes), before it is manufactured. In software engineering, coding is often more a design phase than a manufacturing phase.
Designers need malleability, that is why they all want digital design systems.