1. In the Capabilities callback set these flags

caps["safariAllowPopups"] = true;
caps["autoAcceptAlerts"] = true;

First flag enables the prompt. The second - auto accepts it.  The downside of this approach is that all alerts will be auto accepted.

2.  Use this function whenever you need to accept an alert

function AcceptAlert()
{
	WebDriver.SwitchToAlert().Accept();
	WebDriver.SwitchToParentFrame();
}

Example in RVL

3. If you want to check the Alert text then use Navigator.DoCheckAlert. It will accept the alert if it's text matches the specified string.

https://rapisedoc.inflectra.com/Libraries/Navigator/#docheckalert

JavaScript version

Navigator.DoCheckAlert("This site is attempting to open a pop-up window");

Note: Appium may be slow dismissing alerts but it works.