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karnos, this is a case of specific overriding general.
General: prepared spells must be prepared with the metamagic feat.
Specific: metamagic rods are used at the time of casting and grant you the use of the feat when you cast the spell.
Pathfinder is full of specific vs general "contradictions".
However, if you want to ignore how everyone has understood this to work for the last 5 years (pathfinder) or 10 years (3.5+PF) then that is up to you.
Of course, you can ignore the entirety of the history of Pathfinder (ie: 3.5) and if that is the case you are in trouble. There are A LOT of Pathfinder rules that are not defined or poorly defined unless you look at 3.5 rules.
Example: What is "energy"? If you look just at Pathfinder a case for Positive and Negative "energy" being "energy" (and thus subject to effects that affect energy) could be made.
However, if you look at 3.5 it is well defined that energy is the traditional 4 elements + sonic and does not include Positive and Negative energy despite the name.