Just to be clear, lost numbers do not have a limited life span. They are qualified successes, but no hope of duplicated results, correct?
I can't recall anyone saying the lost commandos only had a few years to live.
Murakami and the other protos only had a short time to live because since they were only practice for Guyot, there was no need to make sure they survived. Same goes for enzyme 1. It was an early design and a flaw with the optimization process that lead to his short life. A scientist told Guyot this and he shrugged it off, saying it didn't matter, it was only a test, and they can fix that issue in the future.
I never really thought of the limited life span as a way to control someone. I always viewed it as, they left that part out because the subject in particular, was expendable, and meant to die. (protos) or cronus was doing new optimization tests to create a new breed of zoanoid, and the process was hit and miss. Some made it, some don't. (Guyot told Tetsuro this the first time they met)