I'm having the same issue with a Pi 3, PiDrive, and the 3A charger. I suspected it might be because I was also using an ATXRaspi board to add a power/reset button, but I did have a 6-foot Anker cable around to test with. I've switched to that one and I get the lightning bolt much more rarely. It only seems to come up on bootup and when first loading a program, where before it was up over 50% of the time when using it.
I suspect a shorter, good quality cable would take care of it.
 Quick followup, I also had an old HP Touchpad charger around that I've had good luck with. I tried that with the Anker cable, and haven't seen the bolt at all. It outputs 5.3v at 2a, it looks like the slightly higher voltage may help, even with the lower amperage.