I see the holes you talk about, but there was never anything in them from new. Are you sure these were not transit blocks that the dealer should have removed.
You have me confused! It would help if you could post pictures of the rubber pads you think I have lost.
Just went and looked at mine, the only rubbers I have are 4 on the underside on the bonnet, none in the described position, but I do notice I have the washer bottle in front of the coolant reservoir on the drivers side, but don't think this should change anything.
Also I too clean my engine bay, as used to keeping my bike engines clean so just because you can't see it why should I treat the 280's engine any less.