I can only really provide you with an answer for the case of the Dutch East India Company, also known as the VOC (Vereenigde Oostindische Compagnie). However, you might find that the general outline sketched here goes for other cases as well.

I think that a possible source of your confusion might stem from the idea that companies such as the VOC were 'colonial' in their goals. The VOC was not an attempt at creating a colony, but an attempt to make money off of trade with Asia. In the Dutch case, from 1594 onwards there were a number of small companies trying to turn a profit by buying goods in Asia and selling them on the European market. There were twelve of these so called 'voorcompagnieën' (a rough translation would be 'predecessor companies'). However, these twelve companies each had a relatively small budget for such a large and dangerous undertaking. Meanwhile, the competition between them was fierce.

That is why in 1602 the government of the United Provinces decided to merge the companies that survived this period of intense competition into one 'United East India Company'. This company was the only one officially allowed to trade with Asia by the government. This way, there would be a larger budget and less competition, leading to less risk and great profit. An added benefit for the state was that a larger company would be better equiped to be of help in the ongoing battle against the Spanish that was the 80 years war.

As you can see, the intent was never to create a company that would conquer a colony. Rather, the goal was to streamline Dutch trade with Asia to increase the profits and to be of more benefit to the state. In practice, the VOC would slowly gain some territorial holdings in Asia to make its trade more efficient (for example by conquering the islands that conquered the most spices. This lead to the nature of the company changing into a more 'colonial' actor, especially in the case of modern day Indonesia and Sri Lanka.

It is these territories that were taken on by the Dutch state when the VOC went bankrupt at the closing of the 18th century. They would then form the basis of the Dutch colonial empire, which was for the largest part conquered by the state. When the VOC went bankrupt, it was nowhere close to controlling all of Indonesia; it was the Dutch government that conquered most of it.

Sources:

Piet Emmer and Jos Gommans, Rijk aan de rand van de wereld: De geschiedenis van Nederland overzee 1600-1800. (Amsterdam, 2013)

F. S. Gaastra, De Geschiedenis van de VOC (5th edition; Leiden 2002)