Have just filled in some deep scratches in a door panel, which were down to bare metal. Have filled with half time glazing putty and block sanded, however the block sanding has left some bare metal spots about an inch in diameter next to the filled scratches. The panel is smooth, feels straight under the hand.

I want to go ahead and prime the panel, but don't know if those bare metal spots need any treatment first? If I understand correctly, factory sheet metal is treated already and most primers can be sprayed over them.

I'm using Nason Select Prime 421-23 and the tech sheet says it can be sprayed over "properly treated" metal

I think it would be strange to spray epoxy primer over just those spots, and stripping the whole panel seems excessive

You can spot spray the epoxy.
I highly recommend you upgrade to the Tamco DTM build primer sold on this site in the Store Front.
DTM (Direct to Metal) primer eliminates the need for spot priming and is perfect for this type of work.

Spraying over small bare spots "might" be okay at times but why risk having adhesion failure? Especially when the tech sheet states "for best results use .... epoxy primer" and requires "properly treated metal."