All of those have discrete codes available. It's possible there is a speaker command in there somewhere that's causing problems with the TV.

Go through your device setup again and when asked, answer that each device has individual commands for on and off. Then you'll have to reconfirm all the activities. Make sure there are no audio input commands involved in the TV activity or device setup (could be the source of the internal/external audio commands).

You also need to turn off Bravia Link (Sync) on all your devices. That is likely the major cause of everything getting out of whack. Bravia Sync (BS) is great if you don't have a universal remote, but doesn't work with Harmony at all. BS does its own power and input switching, then Harmony comes right behind it with its own. Recipe for disaster.

You may have to get Logitech support involved via phone, email or forum (free) to sort out all the details.