well, since the windage tray goes UNDER the crank, you are going to have no issues using it. the pistons and everything else are ABOVE the crank..
you want to keep all the oil in the pan, away from the crank. there is enough oil being flung off the crank to lube everything just fine..
newer VWs indeed do have rifle drilled rods.. never heard of an issue with wrist pin bushings tho, with or without the rifle drilling..