As far as I know, the piston skirts and not the bores are what is polymer-coated. You will see some coating residue on the bores because the purpose of the polymer is to keep the engine from sticking a piston during break-in. By 3000-5000 miles most of the polymer will be gone. So...some polymer residue on the bores is normal. That you see residue also indicates your piston clearance was improperly measured the first time and that the actual clearance is probably right-on. If you had the .008-.009 the guy measured the first time, there'd be no residue on the bores.
Keep in mind that for 02 and later, the reason the pistons are coated is GM changed the tolerance for piston-to-bore clearance as a response to complaints about cold piston knock. The change in tolerance reduces problems with that but it also slightly reduces performance because of increased friction. IMO, the whiners out there who cry about a little cold piston knock have made it worse for all of us hardcore s. I'd rather have a little cold piston knock and the motor a little looser.
Your engine has the revised rings with the napier-face second and the new oil ring expander. All 02 LS6es had them. After the first two weeks of MY02 engine production, all LS1s had them too.