Rob,
I did exactly as you described (base coat then stripes). It was the best way for me given I applied a single main stripe in blue followed by red pin stripes on either side. If I was applying a single color, I would paint the stripe first and then base coat as it is faster with less masking required.
Base:
Look at all the masking required (masked for blue first, then red):
But it looks great after clear and wet sanding: