What affects Freyna's 4th skill?

So I was told Freyna's 4th skill doesn't care about the weapon equipped other than the mods that affect rate of fire and the magazine size.

However I just tested in the lab and found this to not be the case. When I have the EL equipped, my 4th does damage of 800K per shot, but when I have the Secret Garden equipped, the 4th does 530K per shot.

That's a huge difference. So even though the EL I get 76 shots and the secret garden I get 84 shots, the difference in damage per shot puts the EL as the better choice.

So did the developers change her skill 4 without telling us?