I'd like to know how he got 'proto matter' to begin with? Regula I seemed like a pretty remote installation.
The way I interpret it, the Genesis effect didn't actual work, the scientists couldn't make it work according the Carol's theory.
So instead of the Genesis taking regular matter and reorganizing it into different regular matter, it reorganized it into proto-matter. This was done behind Carol's back by her supporters/graduate students under the leadership of David. Just as David had to die for his "crimes," the others who assisted him also died, killed by Khan and his people or Captain Terrell).
All they would have had to do is conceal from Carol the changing of a few thousand lines of code, buried in the greater program.