Here is how we did my exhaust ports on my headers and about the 100 other sets of headers installed at the shop.
Scotch Brite or 3m bristle disk.
https://www.3m.com/3M/en_US/p/d/b40064937/ (Sold on snapon trucks), clean up exhaust ports.
Gasket and rtv. The machine surfaces have some tolerance. The gasket and rtv will take up the slack and compress and seal. Your surfaces look just fine. Torque to spec and drive it.
If you really want your mind blown, take a flat level and see if your exhaust flange on the manifold is flat. 😉