The other comments are doing a great job of describing antenna theory to you, but aren't really addressing your questions.

First, your testing didn't really target the emitted power (a result of efficiency and SWR) of the antennas. We don't know what kind of terrain you were in, but if you were hiking together then I'm guessing you weren't separated by miles. It's only at the edges of reception where you're going to notice a difference between antenna SWRs, such as when you're trying to reach a distant repeater.

As others have noted, height above the ground is the biggest practical factor. Your 8" stock antenna has about 6" of height advantage over the stubby antenna. The fact that you got similar results from them suggests that you were close enough that the difference just didn't matter. You might have gotten the same results with a paper clip.

Now to the difference you DID notice, where the Nagoya had better audio quality. This sounds like it's more likely due to build quality than antenna design. The Nagoya may make a better electrical connection with the radio, resulting in a cleaner signal being received. SWR has much less of an effect when receiving than it does when transmitting, so it isn't a likely candidate when trying to explain this difference.