Pixel ratio (auto saved?)

The settings when you calibrate are saved are saved for the resolution and frame rate combo you are in when you calibrated. These are stored in your guisettings.xml such as…

<resolutions>
    <resolution>
        <description>720x480 @ 59.94 - Full Screen</description>
        <subtitles>463</subtitles>
        <pixelratio>0.888889</pixelratio>
        <overscan>
            <left>0</left>
            <top>0</top>
            <right>720</right>
            <bottom>480</bottom>
        </overscan>
    </resolution>

As you can see it stores both the aspect and overscan. Only SD content should be overscanned though so for all other content your TV should be set with overscan off and there should be no calibration done in Kodi. For SD content which should have overscan I think it is covered fairly well in the how-to on whitelisting that @angry.sardine wrote.