It don't matter if you have 30 qualifications, its wrong
2 flatter surfaces = more direct contact area. Less space for air molecules and other impurities.
If you lap both surfaces properly, they will 'hold' together when you pick one up; briefly at least, in the same way that its hard to pick a CD up off a mirror.
When you have rough surfaces, you cause more of these pockets of air and other impurities to sit between the heatsink and the CPU.
Yeah, TIM helps stop this by filling these, but its basic physics that every time you transfer heat from one object to another, it wont be a 100% efficient transfer (and more importantly, different materials have different thermal absorption and thermal radiation rates) . The more items the heat has to be transferred through, the more efficiency that is lost.
Lapping Guide
Explains it in more detail.
CPU's come with a rough top for a
lot simpler reason: Cost. There is no point lapping a CPU when its not going to make a difference for 99.9% of users.
Now, moving air over a surface to dissipate heat is an entirely different ball game, and is almost always what people get confused with
I have electronic qualifications too, and sadly thermal transfer is rarely touched on in detail (atleast in the ones I did)
Heck, it wasn't until some of the more recent stuff that Fourier's law and Newtons law of cooling was covered