You can, but then you have raw aluminium against the paintwork and that's your only seal against water.
You can't just fill the thread with silicone as they are effectively captive nuts slightly floating under the hole between the two body panels, you have to ensure everything is sealed outside.
The EDPM bonded washers are slightly cupped when not under tension. The trick is to torque them up until they are almost flat but no further. This way they are small disc springs holding the edge of the rubber down and so will keep the seal against vibration and small movements. The centre hole of the rubber is also smaller then the bolt so they are quite stiff, but this means there is a strong seal against the thread.
It sounds complex but when I did it on mine it was straightforward and it just looks right as you do it and see how it seals. One side has been on 3 years the other nearly 2 now and no leaks and the gutters are clear. If I ever wanted to revert I've kept the basic plastic VW blanking bits or you can get them quite easily.
