The other two important gains were due to that Agent Phil.
Firstly, Luke wasn't a mutant.
He had basically confirmed this earlier on.
After all, he had tested it many times, but Daddy System had never added the "X-gene" tag to any of his abilities.
Besides, Carol's Elementary Self-Healing and Iron Hide Creech's Elementary Tempering demanded too many Strength points.
Based on Luke's speculation, Carol was three times as strong as an ordinary person at most, and Creech was five times as strong, but neither of them met the prerequisite.
So, Carol's and Creech's abilities clearly came from their X-genes, while Luke's ability built and expanded on his own basic attributes.
It was impossible for Luke to learn Christophe's Elementary Electrical Control because he wasn't a mutant and didn't have the X-gene for it.
Secondly, S.H.I.E.L.D.'s devices couldn't detect the system's inventory.
