Technically he needs to apply in his country of residence and wait for the D permit to be issued.
But many people have done it the way you describe where you move to Switzerland together and apply for the B permits together. If the non-EU spouse is already living in the Schengen zone it seems to not be a problem.
Of course, this is just want we hear around here. The only people who can give you the official answer are the appropriate authorities.
Good luck!