Berserker wasn't fighting Gilgamesh so much as shielding Ilya from Gate of Babylon. He had to take the full force of the attacks to protect her. Otherwise he would've been able to move around a lot more.
Gilgamesh would still win though probably.
Also I'm pretty sure UBW *can* own most Servants, but unlike Gilgamesh Archer can't just use it forever effortlessly and it takes up all of his power probably.
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