I like flares, like you said just depends where you are, I don't have any rust but I can see it could definitely happen in some climates.
It looks like some bolt on so it'd just be a matter to check are the holes lined up per oem.
To me it'd be easier and probably cheaper to put them back on rather than try to fill holes, smooth, repaint, especially when the paint looks prety good. But I can see it as an option just depending the look a person wants.
Mine are different they attach to the inner rim of the fender with plastic panel retainers. I realize that doesn't help o.p. at all, just, the post make me go look how they were attached. Couldn't determine which models came with them, but it looks like probably XLT 4x4 and STX had them ('97). Again not helpful to o.p. just made me wonder. Maybe the 31" tires (ok, 265/75) triggered them, and those were only available on STX and XLT 4x4.
I think I like the clean look (no bolts showing) and if you look at the '05 brochure I don't see bolts so they must have had a way to attach them without the bolts showing.
Maybe you could get earlier gen flares and attach them to the inner rim, don't know if they'd fit, probably a crazy idea.
2005_ford_ranger_brochure.pdf (therangerstation.com)