While that may feel more right, being Superman does that distance even matter? Shouldn't he be just as capable of popping over?
Depends on the version. Superman's had wildly varying power levels over the decades. The early version could just leap 1/8 of a mile at a time and run really fast, and "nothing short of an exploding shell" could penetrate his skin -- he basically started with the same power set that the Hulk did, albeit a bit weaker. Then it escalated more and more -- he could see through walls, he could fly, he was invulnerable, he could survive in space, he could could move faster than light, he could push moons around, etc. Various retools or adaptations, including the Denny O'Neill comics in the '70s, the Byrne reboot in '86, and Superman: The Animated Series, have tried to dial Superman's powers down to a more manageable level so that there would be more suspense, more chance that he could be defeated without having to fall back on having kryptonite in practically every villain's possession. But usually his power levels tend to drift upward again over time.
So my idea of separating Metropolis and Gotham was predicated on the assumption of a Superman with post-Crisis or S:TAS-level powers, so that a cross-country flight would be a less casual thing than just hopping across a bay. Also, if Metropolis and Gotham were on opposite coasts, there'd be a lot of other cities that would be closer to Superman, and that would affect the relative attention he could give to each. Having Gotham literally adjacent to Metropolis makes it feel like it ought to be part of Superman's extended territory anyway. Most everything that happened there would be literally in his direct line of sight. Even just from a psychological perspective, it feels more right if they aren't next-door neighbors.