2025 Mazda MX-5 Miata Rattling Noise

On the ND2 MX5, Mazda installs from the factory a rubberized coating that starts after the frame rail and pinch weld and stops just before the front and rear crossmember and transmission tunnel. I noticed that 2 very small sections of the (OEM) factory-installed rubberized coating has peeled. I am also aware that Zeibart rubberized coatings and rattle-can rubberized coatings will trap moisture and cause accelerated rusting. However, I do not want to leave these 2 small areas of the metal exposed. The 2 tears in the undercoating are about the size of a nickel. There are no dents. Would applying a little bit of automotive primer followed by applying Rust-Oleum Flat Black Paint be effective? Or, should I apply the primer, add a little bit of Bondo to match the depth of the OEM coating and then apply Rust-Oleum automotive flat black paint? I am also open to other strategies. Please advise.

2008 Mazda miata