I don’t think severing works as well as Lumon would like. We see tons of crossover between innie and outie awareness, even down to simple stuff like Helly R being able to name Delaware, Europe and the equator. The testing floor and Macrodata Refinement seem to be about making severance more precise by refining exactly how much of the complete mind the innie has access to. They are impressed that Cold Harbor Gemma gives no indication of having an emotional response to what they have identified as the most significant trauma of her outie life because the current state of severance isn’t achieving that.

We don’t really know what an innie’s response to being confronted with major outie trauma would be, because the Severed Floor is so clinically sanitized of anything that could possibly resemble the outie’s “real” life. Even when the innies are allowed to do something outwardly normal like a dance party or a funeral, it’s fundamentally weird and wrong because they are avoiding giving them experiences that reflect life on the outside. I don’t think this just comes down to Lumon being incredibly weird, although that helps.

If what MDR has achieved is some sort of perfect severance with no crossover, then Gemma is no longer needed. They can apply this knowledge to all severance from now on and Gemma herself is only a liability: somebody who was kidnapped and tortured for literally years, who the entire outside world believes to be dead. If she gets out and tells people, that’s going to damage Lumon. If she dies (again), they don’t even have to bother telling anybody.