I mean, saying we've won most of our games in the last two years under Klein isn't all that relevant given we've only lost, what, 6 games in the last two years.
That said, I think the whole "refs favour the good teams" argument is putting the cart before the horse. Refereeing decisions aren't random and they don't happen in a vacuum. If you're winning the ruck, getting quick play the balls, dominating possession, your opponent is fatigued, likely bending the rules that little bit more in order to hang on as well as simply being on the side of the ball that necessarily incurs more infringements. Particularly given how we strangle teams it's pretty easy to see how we dominate those stats and the tendency to square up penalty counts seems to have gone away as well. In the time Klein has been reffing, that's mostly not been the case, hence the lobsided stats at the start of his career.
It's not always like that tbf. The Roosters of recent times have been notable for winning while losing penalty counts, but that just shows that they're a team who can absorb a ton of pressure, which allows them to sail closer to the wind in terms of bending the rules when needed.
That's not to say the standard of refereeing is where it should be. Cummins in particular is an abomination, as was Perenara and the game as a whole is in desperate need for simplification in its ruleset. However, in most (not all) games you can generally find the shitty calls going both ways.