The beauty of video games is that, even in the most linear, story-driven titles, no two players will ever have the exact same experience.
Sure, they'll usually all encounter the same beats and set-pieces, but everyone has their own individual ways of playing, and their own idiosyncrasies when it comes to how they interact with the systems developers have created.
Sometimes this results in simple, subtle changes, like the decision to invert your controls (which, by the way, is absolutely the right thing to do), but sometimes a little tweak can result in a radically different experience and, even more occasionally, one that's better than what the developers have programmed in by default.
These games are still amazing no matter whether they're played with the basic options and how the developer "intended" or with some variation, but they can be made even better by changing a couple of options here and there. Consequently, whether it's your first time through or your hundredth, it's absolutely worth the effort to make these simple tweaks that make certain great games even better.