Cannot say I have ever seen this, but Once my Yamaha AVR was set up I rarely mess with it's settings/Menus.

Mine is A9F -> RX-A2070

I have 2 external in(2019 ShieldTV Tube + BlueRay player) but have it connected a bit different. I only have One HDMI from receiver to TV on the Bravia port3.(eARC) The the 2 external sources goes through the receiver first then into HDMI3 on the TV.

So Basically I never switch the TVs input HDMI.. If I switch on the shield or Blu Ray the TV almost always switches to the AVR input, Every Once In a while i will need to manually switch to HDMI3 Input on the TV.. just hit Home to get back to Native TV Apps and eARC sending audio to the AVR.

This way your AVR Menus are always available as well..