I think treating Weyland Yutani as a single homogeneous entity is wrong.
Each division will have it's own secrets and maybe no-one in the main company knows them all. Even within a division there will be secrets and subsections close holed from each other..
I can see it being common place for one section, or even just one person high enough up in a section to try a little off-the-official-books "research", if they thing there is a big enough upside.
I work in the same building, on the same floor, with people I see every day.
Some of these people are my friends but I have no idea what projects they are on, because I don't need to know.
I might guess at the field because I know their specialisms.
As for the other end of the Campus... No idea at all [until the press release comes out].
I think each division needs the others. That's why Burke, who heads the Special Services Division (according to the business card which he gives to Ripley), says that the smuggled facehuggers would be used by the bio-weapons division. Any tech from the derelict ship would be sent to Reverse-Engineering, and then passed on to Manufacturing. Any materials needed by Manufacturing would come from Mining, which in turn would need Terraforming to make the atmosphere breathable and prepare areas for mining operations.
Meanwhile, such operations would involve surveyors, geologists, scientists, engineers, blue-collar workers, security, and their dependents, which means W-Y would also have to work with ECA, the government org tasked with regulating colonies, and the company itself would have to be regulated in turn by the ICC, which handles anything involving commerce and trade (which includes countering smuggling of dangerous organisms). Enforcement of those regulations would involve, among other things, the Colonial Marines, which is also part of the government.
W-Y would also be working with others, such as companies that build and operate space stations and that manufacture synths, not to mention privately owned craft doing things like salvage operations (like the one that found Ripley's lifeboat).
Very likely the rank-and-file wouldn't know what the others are doing, but those higher up, like junior execs such as Burke who head shady divisions tasked to do illegal things like smuggling dangerous organisms (and who is able to order people from other divisions around, like the colony manager, and even order personnel like Bishop, who works for the military because he's tasked to operate vehicles like APCs and the ECA, following production notes, I think), would know a lot more. They were probably even the same inner circles that came up with special orders for Ash to acquire alien organisms alive and intact, and even if it meant making company personnel expendable.
Finally, in his audio commentary to the movie, Cameron pointed out that he wrote the story with the intent of showing companies as evil, and for his references, mention the U.S. military industrial complex and the Vietnam War, the East India Company and colonization of India, and the Bhopal disaster, which symbolizes rich, multinational companies exploiting cheap labor and lack of environmental regulations in poor countries.
