Currently, the mobile site of SFF.SE uses a blue theme, which looks like Super User desktop site color. Switching to red will match the desktop version of this site.
I can’t speak for the SE Staff, but I would guess the answer is no.
Declining as there are no plans to differentiate the sites on mobile (see e.g. the mobile apps).
Since Meta.se is much larger than SFF, and didn’t get an exception, I doubt we’d get one either.
Two additional comments:
If I was replacing the blue on the mobile site with an SFF-specific colour, I wouldn’t pick red; I’d go for a more blueish-grey colour. Red is a highlight colour of the main site; not a main one.
Last I heard, the SE Designers are already backed up for designs for meant-to-be-graduated sites. (e.g. Movies.se, which has been ready to graduate for months with a design pending) Doing a custom mobile theme for every Stack probably isn’t high on the priority list.