How to disable CSS rule in Twentythirteen style.css?

The default behavior for box-sizing is content-box. This is applied when you deselect the rules in Chrome. Have you tried applying box-sizing: content-box in your own CSS file instead of inherit?

.ct-black-square
{
    background-color: #88a0a9;
    box-sizing: content-box;
    -webkit-box-sizing: content-box;
    -moz-box-sizing: content-box;
}

.ct-white-square
{
    background-color: #fdfdfd;
    box-sizing: content-box;
    -webkit-box-sizing: content-box;
    -moz-box-sizing: content-box;
}

box-sizing