That's because the silver particles in AS5 aren't large enough to fit into the machining groove on a typical HSF.
According to calculation the roughness created by 1200grit sandpaper fits the particle in AS5 perfectly.
http://www.overclockers.com/articles1303/
It's the same reason why people get better performance with Artic Silver Ceramique or MX-1 when the metal surfaces is treated at 2000 grit due to smaller particle size than AS5.
The thing is that AS5 is generally more conductive than copper or aluminium.
Wrong. Metallic to metallic contact is the most thermal conductive method.
Overall thermal conduction of AS5 is same or less than actual metal and is only useful in filling in the micro pits.
AS5's conductivity is higher than that of Aluminium and is only just behind copper in conductivity
There will always be microscopic pits on both surfaces and this means that you're always going to need to have "goop" in the middle to provide a connection and as you say.
My unlapped heatsink with AS5 that I applied with my bare finger is keeping my CPU nice and cool at 25 degrees celsius (reported by mobo which of course could be wrong) when the temperature inside is probably about 20 degrees.
With the labour involved with lapping my HS and a going to the trouble of reapplying AS5 by other means you would want to hope that it cools your CPU to a temperature that is lower than ambient.
*sniggers*
Rather than spending a couple of hours lapping your heatsink just put the damn thing in your fricking computer. The increase in productivity from the fact that your PC will actually be turned on will outweigh that extra 3.338758mhz that you get out of it with your "increased cooling"
I could understand someone doing this if the bottom of their heatsink was rough as anything but most decent coolers are fine. and if you bought a low quality cooler then you probably wouldn't care about overclocking anyway!
Just my rant-tastic 2 cents