An idea that might help: post #5 reads like you are manually switching the LG TV to the HDMI input to which the AppleTV is connected... and that is triggering the unwanted event. Have you considered using CEC controls so that when you click a button on the AppleTV remote it basically "controls" the TV instead (it basically auto-switches the TV to HDMI3 in your case)? I don't know that that will resolve your issue but it is easy enough to try.
Also, if you've trained your LG remote to double as controller for your AppleTV, utilize CEC and then the buttons controlling AppleTV to make it request the LG screen via HDMI3 vs. you clicking "input/source" to choose HDMI3 and then trying to use AppleTV.
I suspect there's at least a fair chance that either option will resolve your issue.