Well it might affect performance indeed. And the scale factor that is 1536x960 on the 16" Pro is technically the one that should run the fastest of the lot. But it's a minor difference. On the original Retina devices Apple defaulted to the @2x scaling factor.
Thing is that with all Retina resolutions it will render the actual image at twice what the screen space resolution is, and then if necessary downsample it to fit the display; Actually, slight simplification, some resolutions will render internally @3x before being scaled to fit but let's leave that aside fro now. - So with 1536x960 the GPU power needed is the same as if you were just running the display at 1:1 screen-space and pixel space. I.e. no scaling. With anything else you're effectively rendering a higher resolution image and then scaling it back down to fit the screen's pixels, and since it won't match the pixels perfectly it might also not look as sharp (I am not sure if it's a default, but anti-aliasing can be used to blend in the values from the rendered parts that sit between screen pixels, smoothing things out but still not retaining sharpness the same way as an integer scaling factor. It's a balance where a 2:1 scaling will give the Sharpes image, but to some the less usable desktop space might not be worth the perhaps imperceptible to them difference in sharpness.
Also as noted earlier, media content that has its own rendered resolution will just use the display pixels "directly" anyway, so video and images aren't affected, only UI. It's not a huge deal, pick a setting you like to look at and work with