So what if a frontier model company trains two models, one including 50% of the world's open source project and the second model the other 50% (or ten models with 90-10)?

Then the model that is familiar with the code can write specs. The model that does not have knowledge of the project can implement them.

Would that be a proper clean room implementation?

Seems like a pretty evil, profitable product "rewrite any code base with an inconvenient license to your proprietary version, legally".

LLM training is unnecessary in what we're discussing. Merely LLM using: original code -> specs as facts -> specs to tests -> tests to new code.