Clarifying question: When you say "Pre-CC" what time period are you talking about? Is the Junon Cannon fight part of this?
It seems to me that you're saying that the last Genesis vs Zack fight we see isn't an accurate representation of either of their true strengths. In that case, Genesis's true strength is unknown as is Zack's.
And Zack does not beat Sephiroth. Cloud on the, other hand, is weaker then all of them and he does beat Sephiroth. It is very likely that physical strength has nothing to do with who is the "stronger" fighter.
Cloud stabbed Sephiroth in the back, while Zack faced him head on. Big difference there. And yes, Pre-CC does mean Junon Canon fight. I can also make educated guesses about Zack and Genesis's true strength.
Genesis at the Canon is roughly equal with Sephiroth, but Nibelheim is two years later so Sephiroth is almost certainly on a higher level than he used to be. Zack was able to hold his own for some time despite this fact, signifying that his strength could be on the same level as a person who was Sephiroth's equal two years before.
Besides that Zack at Modeoheim beats the weakened Genesis, and took out Angeal within an hour or two of that (Granted Angeal wanted to die, but still). So Zack is at least as strong as a weakened Genesis at that point, and there is at least another year leading up to Nibelheim in which Zack would continue to gain experience skill and raw strength.
Theres also the fact that a (possibly) weakened Zack was able to beat Genesis Avatar, who would be more powerful than Pre-CC Genesis.
Based on that I can reasonably conclude that Zack is as strong, or slightly stronger than Genesis was Pre-CC
I would also add that strength is exactly what determines the stronger fighter, whereas skill is what determines the better fighter. Being the better fighter does not mean you are the stronger fighter.