I tried this on both firefox and chrome, it was opened in a new window instead of downloading.
window.open("data:application/pdf;base64,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", "mypdf", "width=700px,height=600px");
May be it is related to chrome settings on your machine. Please try from another machine.
Opening/printing pdf on browsers is problematic. Some browsers open using adobe plugin, some uses pdf.js, some uses other methods, some downloads instead of opening.