How come in speedruns Ive watched, they use the Dark beam on Dark Samus 4 when they are shooting back the phazon he expels?
The Entangler also appears. At first, it was thought that this meant the Dark Beam did more damage to her when using phazon, but the Entangler is still the Dark Beam, which is ineffective against the Phazon shield. The weapon just has a habit of surrounding targets whether they're vulnerable or not.
What's really happening is that the Phazon Shot takes on the properties of the current weapon's charge shot, so the Light Beam introduces a meager homing element and the Annihilator, I assume, gives the shot its stun ability... though you'll never see the latter because the Phazon Shot is too strong. The Dark Beam is simply the most visible in this regard and as DS is weaker to the Dark Beam than the others, a connection was made. Any future runs that do this will simply do it for the cool factor or for some reason nostalgia-related.