Metamagic Rods increase the casting time of spontaneous spell caster (of course except quicken spell).
So an spontaneous spellcaster need to use his own metamagic feats just like the Arcane Bloodline metamagic adept requires you to have/use a metamagic you know when use a Metamagic Rod + Spontaneous Metafocus?
To be more specific. Lets say a Sorcerer have Spontaneous Metafocus Fireball and he wants to cast fireball with an Empowered Metamagic Rod (Not using his feats just the rod).