Let them have covert infiltration but don't let them find anything. All the records they find check out (being that the records get altered faster than they can read it), everything appears above board.
The thing is that the company will have to use a different company structure to IoM standard. A bit closer to today's corporations, but rather more benign. It tends towards vertical integration and independence over maximum profit growth.
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1. Some freighter captain is convinced to join the Culture and is replaced with an SC agent looking exactly and behaving like him.
2. Company startup - The freighter strikes out on its own and he starts his own company
3. Culture information advantage allows the freighter to earn lots of money; over the period of ten years or so, the fleet grows into a small freelance shipping corporation
4. 12 years - The corporation sets up its first asteroid mine
5. 15 years - The company turns a few freighters into training ships, crew are trained to be independent, and this includes how to maintain the ship (the blame is put on a Techpriest who 'goes rogue' - read: disappeared)
6. Shortly after that, the company starts a research lab. The lab isn't aimed at discovering new technology, but rather searching for new applications to old technologies. Whatever plans the company cannot buy, its labs put out an alternative, always a creative reapplication of existing technology or a design plan using already present technologies or perhaps a new organization principle. The company begins to shift towards production line styles, inferior in quality to the Ad Mech, but cheaper by an equivalent margin.
6. 18 years - The company is now self-sufficient, it mines its own materials, it trains its own crew (often rehabilitating criminals or poor peasantry), it maintains its own ships. Work begins on constructing a shipyard.
7. 20 years - The company is now willing to take shipbuilding contracts from strictly legal sources (and they are very VERY good at knowing who is and isn't legal), although to the general public, they're just very picky and only take contracts from some people for no discernable reason
8. 40 years - The company has been careful to not cut into other people's trading activities, preferring to develop its own infrastructure. By this time, the company's activities are closely tied to the financial health of many planets and the company's cautious expansion means that while it is greatly important to the planets it serves, it does not move to other areas quickly. The company has a rather large sub-population who work, live and die completely within the company; this population has far better working and living conditions and is far more educated and active than the standard peasant.
Unlike many other companies, this company does not keep its secrets to itself. Competitors, primarily the Ad Mech and other shipping interests, are welcome to look into its structure and even poach its personnel and technologies (although the trained and free-thinking personnel are expensive and well-paid). The company stays ahead of the curve regardless.
9. 45 years - The company begins its first foray into primary research. It focuses on permanent space habitation and logistical technologies (in particular, they have from day 1 a highly expensive project to investigate forcefields for loading and unloading cargo from orbit without a space elevator).
10. 50 years - Rumours of a massive breakthrough in physics begin circulating and the company publishes their records of a few experiments in forcefields which also happen to be the groundwork for the hyperspace drive.