I check yours logs and the vibrations in general are very high (special x -axis) you should dump it. I recommend you to use 3M foam ~5mm thickness, and enable the harmonic notch filter.
Looking to your Bat and Curr logs, when you switch to Loiter, seems that your external governor is doing something different in this mode. Maybe the motor rpms are going back and forward, making the tail vibrating by following the shaking of the motor. I am not familiar with external governors but I see your issue is happening only when your battery is with low voltage and maybe it was just a coincidence, becaue you switched to Loiter mode only when you were running low battery. Maybe you have an issue with your external governor running low voltage and not with Loiter mode. Try the Loiter mode with a full charge battery.