Like many people, I have a CPU heatsink with a flat base that's a square comprising alternating strips of aluminum and copper heatpipes.
Imagine adding layers of aluminum to this base. That would surely interfere with the heat sink's ability to remove heat, since the copper is further removed from the CPU and a worse thermal conductor, aluminum, is in the way.
Now imagine adding solid layers of copper to this base instead. That would still interfere with the heat sink's ability to remove heat, because heat pipes are MUCH more efficient than an equivalent volume of solid copper. The copper would get in the way of the heatpipe liquid removing heat.
If these things are true, then it makes sense that removing copper from the heat pipes at the base by lapping them would improve access to the heat pipe liquid. Even if your base is flat, further lapping would improve the heat sink.
Of course, if you lap it too much then you might rupture the heat pipe, which would be harmful!
I did a half-assed job lapping my heatsink and stopped because I was afraid of rupturing the heat pipes.
I'm not sure if the lapping helped because it's flatter now, or because material was removed as explained above, but it made a difference.