If the intake manifold was changed for the SE-R in 05 it certainly wasn't in any press release that we saw. Any manufacturer tends to be pretty tight liped about the sources of power increases. While we can't confirm or deny (do we sound like the FBI or what) the intake manifold was changed, our belief is that the most likely source of the found power in the Altima SE-R is in the exhaust system.
Look at the examples on a Stock Altima SE (close) vs. the Mossy system.
We would certainly hope to see more power out of the car if the intake manifold was changed. Then again, with all that power going to the front wheels the car really doesn't need much more power.