So I finally ordered my new audio system. I'll get it on Tuesady!!  I discarded the soundbars and went for a Yamaha YHT 4940 which supports DTS-HD and Doby TrueHD in 5.1.

It has HDMI/ARC and 4 HDMI In ports with 4K/HDR 4:4:4 video passthrough so it won't be an issue to get the right audio from the HDMI devices. What about the audio from apps like Netflix, Plex, Kodi, Amazon Video, YouTube etc.? Does the audio get sent back as it is, with the apps automatically choosing the best audio format supported by the receiver? 

I know Plex has some specific options, but I'd like to know (in advance, before getting mad when setting it up) how it works in general, being quite noob on the topic. Plus I'd like to understand what does not work due to some bugs, as I keep reading around.

PS: Connecting the PS4 to the receiver and then to the TV would add any input lag?