To center two plots, you can add fig.align='center' to your fragment settings. If he creates one chart over another, add also fig.show='hold' . The result should be two centered graphs. 
So, you, the last option, should look something like this:
{r,echo=FALSE, out.width='.49\\linewidth', fig.width=3, fig.height=3,fig.show='hold',fig.align='center'}
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