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Reality says

Do you not realize individual workers can quit the company and seek employment elsewhere at any time? It's nothing like a nation-state or even a slave plantation. The so-called "top-down" organization in a company is voluntary association; i.e. still a bottom-up organization. The owner of the company simply owns the passive capital stock of the company (therefore at a disadvantage and have to be protected by property rights), not the individuals. That is very different from a top-down nation-state (where membership is mandatory), which inevitably comes down to slavery of one shade or another, centralization of power and all the leaders killing each other to grab that power, with the worst scum eventually floating to the top!

There is only 2 ways to organize: bottom-up self-organization (like happens in evolution, there is no central control and order 'emerges' from the interaction of the parts), or top-down design (intelligent design, i.e. 1 central designer controls or at least influences the parts). It's not different, whether you are talking of companies or nations, or even design of species.

Human beings have lived in tribes and evolved a cognitive bias to obey their leaders, because it is critical for the survival of tribes. This is this bias that is hijacked in personality cults, whether in states (Stalin), or politics (Trump), or religion (Jesus). But without strong leadership armies cannot function, companies drift into irrelevance, the Hebrews would never have reached the promised land, and Shackleton's men would have died in Antarctica. Leadership is the central control, the coordination, that is vital in all these situation.

This doesn't mean we don't need self-organization. We absolutely do. No one at the top of a nation controls every details of the economy and people's lives. Better let people on the ground deal with complexity on individual situations.

However saying this doesn't negate either the role of leadership. Top-down leadership is still vital. The key is to be able to tell when one is better than the other.
Claiming top-down is always a bad idea is absurd.

There is a huge difference between Leadership vs. Top-down Coercion. Even among the examples you gave, neither Shackleton nor Jesus exercised Top-down Coercion; they carried out their leadership through inspiration, inspiring their followers into voluntary action. Stalin of course took the coercive state secret police approach. If we have to venture into contemporary politics, Trump is closer to the former approach whereas his political opponents are closer to the latter . . . which is the reason why his political opponents are losing badly world-wide.

"Intelligent Design" would only work if the designer is Omniscient and Omnipotent (i.e. God). Obviously no human being has that kind of qualification. Evolution from the bottom up is the only way real progress can be sustainably carried out in human society. In the relatively backwards societies, such as France (compared to England in late 18th century), Germany and Russia (compared to western Europe in the 19th and early 20th century) and China (compared to Europe and America in the 20th century), the local elite's access to textbooks translated from the advanced economies/societies in other parts of the world may give them a (false) sense of God-like knowledge superiority over their countrymen, just like parents over kids in childhood, teachers/professors over students. The copying may indeed goose the local formerly backwards economy very quickly as the "design" had already been carried out in a different country. Those carrying out the copying may think they are doing "Intelligent Design" . . . however, the implementation is almost always very flawed: the rapid progress creates unrealistic expectations about the natural speed of progress that can be sustained when there is nothing to copy. For example, Japanese economy has been stuck for 3 decades after the copying phase was over; Karl Marx mistakenly thought linear progress (hence "progressivism") was the nature of human society instead of cyclicity, and his followers not understanding that "end state" is literally death: life/living is a process, nothing pleasant about jumping to the "end state" / death. Massive bloodshed awaited French, German, Russian and Chinese when what could be done with copying was coming to an end and there was no native creativity to sustain the unnaturally rapid economic advancement that the local population had grown accustomed to in a few short decades of copying. That is a recurring theme in human history.

Company leadership is about individual responsibility: the owner of the private property has to exercise his intimate knowledge of his capital or the workers would choose to work for someone else. At no time is the owner of the factory allowed to coerce his workers.

The military context is affected by the N-Squared Law, so co-ordination and timely application of as much available force as possible on the enemy is of critical importance. People who are not familiar with military operations may think top-down structure makes military efficient . . . that actually is not the case. The first thing you'd learn in a staff college for training officers is how to inspire local individual initiative. One of the primary reasons why American/British, German and Israeli army units are much more effective than comparable units in their opponents is the emphasis on local initiative and decision making. That is fundamental to Bewegungskrieg. An army accustomed to following orders top-down is one that gets liquidated like the Soviet post-Stalin purge army at the opening phases of Barbarosa and the Egyptian 3rd army getting rounded up at Sinai by a smaller opponent.