In the comic, it took several issues before Nathan finally realized that his Professor was in fact, the mystery cyborg.
And for a comic book, that extended period until the revelation came, was very fitting as Nathan and Malakai had built up a pretty close, mentor-student bond, making their bitter confrontation, all that more heart-wrenching for Tech Wiz.
But for a live action adaptation, that extended period of time was a luxury they didn't have.
For a movie that was planned to be a two-hour, thirty minute+ epic, if they tried to fit and squeeze the bond that Nathan and Malakai built over the several issues in the comics, it would just end up feeling somewhat forced, undercooked and generally unpalatable to the audience.
As a result, Kyle had seriously been pondering, way before the live action adaptation was even greenlit by him, same as Xavier whom had stumbled upon the exact same conundrum after Kyle had gotten him on board;