I can't speak to the specifics but I'm pretty sure the differences are statically significant, despite the AC difference being a small number.
And overall you're right, that 500 heights don't always translate to sensible weather. QPF is not a good metric for models. It's better than it used to be, but still one of the worst variables to predict. Typically models are better at finding a window QPF will occur, but bad at finding the right amount of QPF.
Think of it this way. Whether you get a wound up coastal with 1" QPF or a fropa with 0.01" in snow showers the model still had the trough for that period. High AC score, low QPF score.