I think the Rust Bullet stuff may work better for this.
I would think the paint should be taken off in the areas and then treated/painted (no matter what product is used).

My neighbor was a Chrysler Service Manager a couple of years ago.
He said that Chrysler almost never covers rust under warranty unless it has created a hole from the inside to the outside.

Under warranty:
Has anyone had their doors replaced c/o this issue?
Anybody had their trunk or SRT6 wing replaced c/o this issue?