The stage I worked at Iron Sights Nationals was a fixed-time stage...with turning targets, so no timer was used at all. That worked very well and allowed us to run four shooters at a time and get through entire squads in about 12 minutes.
With other fixed-time stages the second beep can be an issue, as you note. It is certainly a best practice, basically mandatory, for the RO to be near the shooter for the second beep. However, even if the RO does his/her job correctly, it can still be hard to hear the second beep, particularly if a shot is fired at the exact moment of the second beep. One thing that mitigates problems with not hearing the second beep is that the penalty for overtime shots is just 5 points (it's the only 5-point procedural in USPSA), so if you shoot alphas with your overtime shots we basically just take away the alphas. On turning-target fixed-time stages, like the one I worked at Nationals, there are no overtime penalties.
I have heard that AMG is working on a speaker/bullhorn type of device that can be used in conjunction with their timer for fixed-time stages.