My honest guess is that they added a couple of spaces in between the action in stage one in order to make the music line up a little more dramatically to when the first boss appears and when he starts firing missiles.
It is some sweet music, though.
Also, I wish I could have been in the room when they planned the first boss.
"Our gloomy futuristic alien invasion shooter on premium hardware with an 8mb ROM is going to feature a massive multi-jointed animated robotic boss in the first stage that has a head sticking out of its butt."