Thanks for your reply bgmeek,
I have been controlling the Apple TV with my phone for the past few months after my kid accidently dropped and original controller and the screen shattered.. I did not know it was made of tempered glass. I made a mistake by throwing it away too, cause then I could not set up the Apple TV after resetting it, but I solved this issue by borrowing a remote from a friend as urgent solution.
In short, everything works perfectly fine when I don't turn off the TV and Bose System (they seem to be linked together because when I turned on one of them, all of them turns on, and vice versa), and the system will also turn on/off the Apple TV automatically.
The muting problem only happens at the beginning when I just started the systems.
My current only solution, besides restarting the Apple TV is to
return the Apple TV to home screen, from whatever app it was playing from, and I had to scroll randomly until I hear sounds from the Apple TV.
Doesn't this sound like a bug?
Could this be the software/firmware problem from the Applet TV? Because I have no problem like this with other devices connected to the Bose, such as PlayStation, Switch and Satellite TV.
But come to think of it, before I got the Bose system, the Apple TV was hooked up directly to the HDMI port on the TV, and never had any issues.
Or maybe these two systems just have problems with each other.