Oh, I wouldn´t -or let one player- do it but I was wondering if the rules technically would allow it. Actually, metamagic rods "confers [...] only the ability to use the given feat a specific number of times" I´d say that the caster, if he´s not a spontaneous caster, still has to prepare the metamagiced (sp?) spell in the normal way, only that the level is not changed. And when crafting items , the SRd says "The act of working on the [item] triggers the prepared spells, making then unavailable for casting during each day of the [item]´s creation (That is, those spell slots are expended from his currently prepared spells, just as if they had been cast)" Scribing a scroll does not only use the spell, actually "casts" it.
Actually, I´m thinking that this question applies too to abilities and epic feats that allow the reduction of the increased level for metamagic.