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640×480 default is set because higher resolutions will slow down rpi1s. In the past display resolution was switched which caused flickering and was not compatible with all screens. Rpi2 and 1080p should be fast enough if you use no shaders. Rpi1 and two share the same default configuration at the moment.

If you have a 16:9 screen resolution and 640×480 render resolution retroarch will increase your horizontal resolution to 853×480. So there should be no unequal pixels since Retropie 2.6 or 3.0.