Yes but the problem you cite is a problem you are intentionally creating with those CHARGEN examples. In real life who's going to be a great pilot and not be a great pilot? I understand the rules mechanically allow it in the game, but intentionally building a character to not make sense isn't the rules fault. A PC is in charge of how their xp is allocated and there is no RPG that prevents someone from making a character that sucks, or is a walking oxymoron.
The examples I cited are extreme, certainly, but deliberately so. The problem exists even when a character has been deliberately created as a pilot - their skill is still hardly relevant, only their talents. With the same talent build, shouldn't a pilot with Agility 4, Piloting 4 have the edge over one with Agility 3, Piloting 2? I don't see how they will in the rules as written.
I am not sure what you are reading in the rules to suggest that the stronger pilot has no edge over the weaker pilot in this example. The stronger pilot will succeed more often on piloting and gunnery skill checks than the weaker pilot (presuming of course the same logic is followed in your example with regards to ranks in Gunnery).
This does not mean the stronger pilot will win **every** encounter with the weaker pilot, and that is how it should be.
I'm not saying that the "stronger" pilot has no edge, I'm saying that "stronger" means talents, not skill. There aren't many Piloting rolls required unless you run all your space combats in tight terrain, so unless you've got one of the chosen few specialisations that give you the right talents then you're largely helpless.