lapping is when you use sandpaper of increasing grit levels (up to as high as possible) to give your IHS a flat and mirror like finish. and no it wont live, you can pop an IHS easily enough but you have to be extra careful with the chip from then on
its just the way they are, dunno why (there might be a reason). generally anything other than 100% flat is seen as a defect and should be sanded out on a really flat surface (usually glass) to give a slight performance bump. also the mirror finish means less tiny air pockets on the surface = better conductivity and the sanding removes anything that the copper is coated in