I mean, I feel like the answer is pretty easy. The Trunks we see mopped the floor with the androids when he went back to his timeline. The Trunks that Cell killed wasn't as strong. Remember, Cell's Trunks was caught off guard, he'd never seen that creature before. The Trunks we see went into the hyperbolic with Vegeta specifically to battle Cell
We never see what the trunks in cells timeline did, I was under the impression he went through the same steps as the trunks we see Minus cells existence, plus they trained in the hyperbolic time chamber to defeat the androids, not just cell specifically, which could have happened with the trunks in cell’s timeline, it was just never explained
