You're wrong. Even if you ground the surfaces down to the kind of tolerances the best prosthetics use (joing replacements), you would still need to use a lubricant. In fact, these kinds of devices still have so much friction, that without sinovial fluid they rapidly break down (and even with still only last 5-10 years on average). That's of course due to microscopic imperfection in the mating surface. With regards to heatsinks, the point is that even with that kind of fine processing - which is impractical by hundreds of orders of magnitude - you'd still benefit from some sort of thermal interface.
You are right, no lapping would ever be perfect, but im not saying you should do so and fix your waterblock / heatsink without one.
Most of the time, the IHS is not flat, and you have a few options to "fix the problem".
1. Lapping and applying a thermal compound
2. Like ruyven_macaran said, remove the IHS (but i guess its not really recommended
3. Just apply thermal compound
And as far as i am concerned, thermal compound really matters when we are talking about the third option (or the second, i dont know how uneven a processor die could be). The whole idea of lapping is to make a direct contact between the IHS and the heatsink, thus making thermal compound less important (you sill HAVE to apply it, but does it make so much difference between brands?).
But i agree with both of you. You cant get rid of these tiny cracks.