Can you apply a waterproofing over semi-transparent stain?

As long as the stained surface is porous and in some cases has weathered for at least 6 months you should be able to. Follow all manufacturers directions though to be sure.

You can check if it is porous by spraying it with water. If the water beads, no need to waterproof it. If it soaks in, it should accept a water proofer.