Acidic rust converters won't work on an area that has no rust. There's no iron oxide for them to convert. Your best protection on unrusted metal surfaces is an etching primer covered by a good paint system.

Rust neutralizers are generally flushed off with water and dried. No other special treatment is required other than good etching primer and paint.

You should cut out bad rust, convert minor rust and pitting, and treat unrusted metal for what it is - unrusted metal.