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The AESA antenna is actually positioned higher than the bridge, and the two radar systems are installed on both sides of the ship to prevent obstructing the view from the bridge.
Indeed, it's certainly positioned in as practical a position to minimize coverage of the bridge as much as possible, but by nature of the lookdown/surface search emissions, it's still going to end up flagging a decent chunk of the superstructure -- unless of course, it is programmed not to.
