I ran a fingernail over the base of the heatsink and yesh that machining sucks. When I did this on my Zalman 7000-AlCu it was pretty smooth (the Alpha PAL8045 I used to have was even better!) but the VGA Silencer's base was downright rough.
So I detached the plastic from the heatsink and started sanding with some 400 grit paper (I did this on a marble counter) when I realized that this thing isn't even flat. The base was significantly concave

So I busted out the 150 grit and sanded this thing down until it was flat. Then I worked my way up to 2000 grit sandpaper. End result was much smoother and flatter than the way I received it.
I'm not sure it makes much of a difference this made in the end (I applied Arctic Silver 3 afterwards), but I'm sure wondering why this wasn't done right from the factory...