The problem with colonialism is exploitation of the people, not the setting up of a just government. I'm in favor of Western countries coming in and setting up a just government, even if there is a profit motive involved. It at least is much better than a constant war torn and corrupt environment.

Where would the justice derive from in a government that was set up for the purposes of extracting resources in one area and transferring the resulting resources and wealth to a different area?

Justice as in peace is brought to the local population and they are kept from murdering and stealing from each other. Whether they get to keep their local resources or not I think is a secondary concern to whether they have a peaceful society.

Very Hobbesian. I think you'll find actual implementations of the systems you propose don't really discourage murder or theft; those don't concern the bottom line. I'll point to the Belgian Congo as a relevant example in this space

I've heard that some previous colonies have done quite well after the colonizers left, when the colonialism was combine with Christian missionary activity.

In more ancient history, while the Spaniards did many horrible things to natives, they also put a stop to even greater horrors, such as the mass human sacrifice at that time.

Even further back, Roman colonization was exploitative, but did also bring peace to the different regions they colonized.

So, colonization can bring about a better social structure. Given that people are often driven by selfish gain, getting something out of enacting a just social structure seems to be the best way forward.

False dichotomy. Or Strawman. Both apply.

I don't think that it is.

If you look at what the PRC is doing to establish footholds and reliable supply chains, it bears a strong resemblance to those old trading companies. The US does various "counter-terrorism" operations in different countries, essentially borrowing African military units.