Shouldn't be a problem with exhaust protrusion, after all, motorcycles don't have them covered at all.
You could always add a shield over them if you wanted. Check out this 250SWB, it's got a shroud over the pipes on one side (to stop fuel spilled from the filler above getting onto the hot exhaust) -
When it comes down to it, just pick an exhaust style you like and make it happen. That's the joy of building your own car!