The Ford rust warranty only covers penetrating rust originating from inside
the panel; rust caused by damage through use, or even badly fitted
components, is not covered.

If it is obscured by the splashguard anyway it will be a fairly easy fix as
there is no need to match the paint.  Rust treatments are OK, but much
better to abrade it all back to bare metal and fill / reprime it if you can,
or a local garage / body shop probably wouldn't charge a huge amount.