@swagpack: You do have to bear in mind that this isn't a real universe, rather a digital one, and it is not actually a full size universe (at least not in the way that ours is) instead each area is an individual reality marble sustained by the Moon Cell. BB is an AI that IIRC became cancerous and started advancing eventually expressing a degree of control over these digital environments/universes making her essentially a reality warper within the Moon Cell. However for some as of yet unidentified reason, Gilagmesh was always an anomaly and difficult for the Moon Cell to deal with, BB did not possess the capability to erase Gilgamesh and Gilgamesh possessed Ea - which is of course able to crumble reality around it and reduce creation to nothingness.
BB did not possess a counter to Ea - very few things do actually - and her powers where not all that effective against Gilgamesh, this is more a testament to his destructive potential and unique unconventional existence in the Moon Cell but it doesn't mean he is actually on the level of a reality warper. Statistically, besides his Noble Phantasm, Gilgamesh was (similar to all other incarnations) among the lowest of Servants IIRC (especially considering for the most part he was weakened).
Main point being that the nature of the Moon Cell being digitally based and BB's powers centering around that fact, coupled with Gil's ambiguous immunity/resistance to her manipulation, means that it's all difficult to apply to a universe outside the Moon Cell.
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