"There's no way the entire company is going to gather all of the engineers and everyone around, have them code up a secret system "

No, that is why I wrote

"Who would really know, if the pipelines are set up in a way, that only very few people are aware of this?" (Typo fixed)

There is no need for everyone to know. I don't know their processes, but I can think of ways to only include very few people who need to know.

The rest is just working on everything else. Some work with data, where they don't need to know where it came from, some with UI, some with scaling up, some .. they all don't need to know, that the source of DB XYZ comes from a dark source.