I painted the rear resonators on my '11 Overland Hemi with heat resistant paint, stayed good until I traded for my SRT last month.
I used chrome polish on the pipes that you are concerned with to clean them up a bit, thought that looked good, but no reason that black paint would not work there as well.
I used Rust-Oleum 2000 degree primer and flat black paint which basically makes the pipes disappear. Wipe the pipes down with solvent before priming. Good Luck!