The issues is that it no matter how clear pla is it still refracts light. This causes light to be slightly redirected every time it enters and leaves the pla. Because a 3d printed object is made of hundreds of layers resulting the resulting finishes similar to privacy glass. So it may not be what you were expecting.
I would suggest printing a mold and using a clear resin to cast your clear object.
You CAN however tell your slicer that your nozzle is wider than it actually is. You may need to slow down printing speed but otherwise that works fine because it will just push more plastic out. With a 0.4mm nozzle you can set a nozzle width of, say, 0.6mm and a layer height of 0.45mm.