I figured out when this occurs, and how to work around this issue. As I mentioned, above, when I plug my phone into the controller (notably, after the controller is already powered on), my phone vibrates like it normally would when you plug in the charger. If the screen isn't on when I do this, the battery charging meter is also displayed, which also indicates it's trying to switch to charging mode (which my theory is why it drains the battery, since the conduit for charging is open, allowing power to flow in either direction).
However, when I plug my phone into the controller before powering on the controller, then launch the DJI GO app, then power on the controller after the phone is connected and the DJI GO app is launched I don't get the charge vibrate indicator and the phones doesn't drain. I have tested this several flight with no phone drainage, which validates these observations and theory.
I've gone from the phone losing 45% charge in one flight to 20% (running down Mavic to 8% and with full screen brightness and without Battery Mode turned on). Also, the controller is discharging normally (~15% per flight) versus maintaining 100%, also indicating it isn't being charged by the phone like before. So, after 3 flights, I'm still at 40% phone battery, which for 45 minutes of constant video and full screen brightness isn't terrible (not great, but beats the phone dying). I'm sure this would improve slightly if I turned on Battery Mode to limit background processes which is probably a good idea anyway while flying. I'll try this next time I'm doing 3 flights back to back and see where I end up.