The only time I get three beeps is when I get too far away from the car too quickly (i.e., before the "I'm ready to lock now" beep goes off), which means I have to use the remote to lock the car instead of having it lock automatically. I've learned to hesitate for a beat after closing the driver's door before I step away from the car, and that has always worked.
I'm not sure I've ever used the handle to open the rear hatch. I either use the button inside the car if I'm getting out, or the remote as I approach it if I'm getting in. Or if my hands are full, I'll use the kick method. But in general I hate just standing there waiting for it to open, so I do whatever will get it started before I get to the back.