Okay, I checked each of those scenarios and the lights still didn't work, but... After an interim of ~24hrs, during which I restarted my computer, I compiled the same map under the same settings and the lighting worked. Unfortunately since I let so much time pass I didn't have a controlled environment to tell me what exactly fixed the problem, but if I come across it again I'll post here and try to get a better grasp of what's causing it.
On a side note: Does rotating the light_environment entity in the viewport change the angle of the sunlight in game? I know there's yaw pitch and roll entity properties in the command panel.
On a side note: Does rotating the light_environment entity in the viewport change the angle of the sunlight in game? I know there's yaw pitch and roll entity properties in the command panel.