I think OP brings up a decent point that did confuse me as well. Between written descriptions and animations, there may very well be plenty of room for error and misinterpretation but I will use the mentioned point OP presented for the purposes of comparing.

The M61 vulcan does indeed have an fire rate of 6,000RPM (100 rounds a second) and a muzzle velocity of roughly 1000 meter per second. "It's not a noble phantasm" can not be used as an argument in this case since Berserker turned the entire aircraft and accompanying weapon systems into his Noble Phantasm. What the weapon system does have against it is that it's linear fire unlike the Gate of Babylon, so it relies on the weapon's lack of accuracy at increasing range to saturate an area with fire.

The Gate of Babylon can fire from multitudes of angles and (going off animation design) seem to have roughly standard bullet velocity. In the same scene OP is referencing, Gilgamesh apparently has three of them arc to attack Berserker in midair from an angle. Also, what makes it much more lethal is the size and shape of the projectiles being hurled, considering bullets are made to be aerodynamic to achieve their velocities and accuracy but the GOB's projectiles don't suffer from this setback to achieve theirs. However, every time he opens the gate we're almost always able to count the number of 'shots' he's firing, and a vast majority are no where near the area saturation the vulcan can output.

With how it was animated in Zero however, it seems they dramatically reduced velocity and RPM, either for visual purposes or something else entirely. The weapon's spread also seems to have increased to absurd proportions when he sweeps in to roughly sea level when firing on Saber, but this could have been due to mad enhancement and blood-lust induced tunnel vision. She seems to be dodging at near point-blank range as well which would further OP's confusion.

So, animation aside, I believe the reason the GOB is portrayed as significantly more dangerous than a NP'fied vulcan is due to the mad enhancement's (supposed) degradation of the weapon's accuracy and Gilgamesh being able to change the gate's firing angles and in-flight trajectories on a whim; Dodging 10 rounds that can change angles and hit you isn't as easy as finding the opening i na curtain of incoming rounds. This is just my take on this though.