If gsync is enabled for windowed applications in the nvidia control panel it actually synchronizes to the active window not the rest of the OS. This can actually be pretty problematic if your not a single app at a time user which is why it defaults to turning on just fullscreen gsync when you toggle it.

Hardware acceleration or not probably doesn't play into it as much as how abstract are the layers i.e. are there 4 layers of hardware abstraction library to make the app work everywhere which use it's own buffering to stay smooth regardless of the underlaying system and then hands that to the OS which then buffers it as part of the compositor to be displayed or does something just blit "n" to the display framebuffer as the latter is likely to have less delay/jitter.