Thanks to Etienne for the code to set blanks as gaps. I got help from a POI developer and here is the solution that solves both issues mentioned in the original question.
XSSFChart chart = (XSSFChart)drawing.createChart(anchor);
// this will set blank values as gaps in the chart so you
// can accurately plot data series of different lengths
CTDispBlanksAs disp = CTDispBlanksAs.Factory.newInstance();
disp.setVal(STDispBlanksAs.GAP);
chart.getCTChart().setDispBlanksAs(disp);
// setup chart, axes, data series, etc
chart.plot(data, new ChartAxis[] { bottomAxis, leftAxis });
// this must occur after the call to chart.plot above
CTPlotArea plotArea = chart.getCTChart().getPlotArea();
for (CTLineChart ch : plotArea.getLineChartList()) {
for (CTLineSer ser : ch.getSerList()) {
CTBoolean ctBool = CTBoolean.Factory.newInstance();
ctBool.setVal(false);
ser.setSmooth(ctBool);
}
}