I was googling my question and found addUIInterruptionMonitor method:
app.launch()
addUIInterruptionMonitor(withDescription: "System Dialog") { (alert) -> Bool in
alert.buttons["Allow"].tap()
return true
}
app.tap()
We only have to enter an appropriate description and the necessary button title.
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@chbeer, it works for touch id only. For face id and optic id users (in our case, automated test) have to tap some button in the alert.