The annoying part is that App Nap also does this with plugged in desktops or even worse with servers that don't even have a monitor plugged in. At least it can be disabled systemwide.
Throttling background apps has its place on a desktop, too - leaving aside power efficiency, there are material performance gains to be made when the OS automatically prioritizes foreground tasks. I wouldn't want FCPX rendering impacted by a rogue banner ad on HowToAddLensFlare.co.cz, know what I mean?
I can see how it might be problematic in a headless environment, but for most people most of the time it's probably a useful feature.