The modal that appears with the "Call (123) 456-7890" "button" and Cancel button belongs to the Springboard app. So if you attach to com.apple.springboard in your XCUITest you can check for a *label* with the "Call ..." text. For some reason that is actually a label/staticText and not a button.
func testCalling() throws {
// launch our app
let app = XCUIApplication()
app.launch()
				// trigger the app's call to OpenUrl
app.buttons["Call"].tap()
let springBoard = XCUIApplication(bundleIdentifier: "com.apple.springboard")
print(springBoard.staticTexts.allElementsBoundByAccessibilityElement)
}