The output will be slightly worse, but at 400 PPI you probably won't be able to tell without a magnifying glass. The current Retina MBPs do this in their higher res modes and it's pretty hard to notice.
On battery life: perhaps the tradeoff of using a 1080 panel outweighs the scaling.
Also it leaves the door open to switch to a full resolution native panel in an iPhone 7+ with no hit to existing apps or developers.
I do hope that there is some sort of programmable setting or API for enabling native resolution output so that games built with this option are rendering at 1080p and displaying at 1080p, or 1080p movies aren't needlessly being stretched and then downsampled. For legacy apps and not graphically intensive stuff it mostly makes sense to just display at 3x and scale down for simplicities sake, but if the option isn't otherwise there that seems pretty silly.