I don't yet have any naim products, but I have an atom on order (I'm being given a due date of Feb atm for a HDMI one). I'm also moving from 5.1 to stereo and have been running my denon amp in 2.1 for a few months now in prep. I have a cheap sony bluray and an appletv plugged into my LG tv and I have some apps o the tv itself which seem to work well.
I'm sure the optical connection will work fine, though I'd investigate getting the HDMI card for your atom if you don't have one. This should allow a level of comms (HDMI-CEC) between the TV and atom so when you turn the TV on, the atom will come automatically and set input to the audio return channel (ARC) from the TV, and the TV remote should control volume on the atom instead of the TV. The fact that the atom comes with a HDMI port was a complete show-stealer for me because of this.
For movie watching, I usually use netflix and amazon prime on the telly, but I also have a plex server running with the app on the TV as well. I also have the apps on my appletv.
To your questions
1. that would depend on the film and your preferences but I imagine most people would go for the best one. 7.1 truehd or whatever. Unless there's a dedicated stereo track just take the best one, it'll get downmixed to stereo by the source device anyway (see below)
2. That would work but as you say, not very intuitive. I've used both kodi and plex and found them generally excellent. If your TV has a DLNA client, then you could always run a upnp server and let the TV get your content that way, but then you have to be confident that your TV can deal with any codecs in your files.
3. for kodi, you could always get something like an amazon firestick or roku and install kodi (or plex) on that. it should have a better remote. Also, if everything supports HDMI-CEC then you'll probably be able to use your TV remote to control kodi and plex. (I don't think macs support CEC sadly)
4. I personally like and use plex for videos files. I use the app for my TV while it's supported. if it goes out of support then I have the app for my appletv as well. The ios client may well be transcoding, but you should be able to see what it's transcoding from and to in the server webpage. Generally with plex, if the client supports that audio or video codec then it'll send it through as-is. If the client does not support the codec then it'll transcode one or both. Video transcoding is hard work though any modern CPU should be fine with it. Audio transcoding I doubt would seriously tax any cpu from the last 10 years. Appletv's have relatively restricted codec support which might be why the audio is being transcoded.
For audio, I'd suggest using a uPNP server. your atom supports almost every codec anyway so doesn't need the transcoding, and you'd probably like to use the naim app rather than the plex or kodi apps. as it happens, plex runs a DLNA server as well so the naim app would be able to see your audio served up there, but I just use minimserver which is free and more focused on audio.
A couple of notes.
the appletv is a lovely device but it might not be ideal for audio as I believe the audio output is fixed at 48khz, so any other frequency would be scaled to that. the atom will play everything natively.
secondly, for films, you should expect to lose a bit of bass, even if you're augmenting stereo speakers with a subwoofer. this is due to the downmixing process and I've got to say, I think it's a bad design decision back in the history of surround sound. Let me explain.
think about a 5.1 film soundtrack; 5 full bandwidth tracks (L, R, C, SL, SR) and a limited bandwidth LFE track. Note that the LFE track is not designed to be a dedicated subwoofer track, though it is usually taken care of by the sub. When your DVD/Bluray sends a 5.1 (or 7.1 or atmos, whatever) track to your AV receiver it will look at it's speaker configuration and route the audio appropriately. If you have a 5.1 speaker setup then what usually happens is that it routes the LFE channel, and all the audio under (say) 80hz from the other 5 channels to the sub.
If your DVD player is connected to a stereo amp via phono's (or dgital to a stereo dac) then the DVD player itself must create a stereo mix to send to the amp. There are default rules for how to create this and the audio track engineer can influence that process too. The rears are usually mixed into the front on either side at a reduced volume and the centre channel split to LR with some processing. the LFE track though is just dropped. It is not mixed into the stereo downmix by a source at all. The reason for this is that the LFE channel is actually mixed at and can go 10db higher than the other channels, and is designed for ultra low frequencies. There was a concern that if they mixed this into the stereo mix that speakers not capable of going down to 20hz (which is almost *all* of them, very few speakers can hit 20hz at a reasonable volume, I can think of one off the top of my head) might suffer damage from being over driven. Also, many people watch films using their TV speakers which can barely hit 100hz, never mind 20.
This argument sounds sensible until you find out how an AV receiver configured for stereo works, which is that it performs a stereo downmix like the source, but it knows what speakers you've got. If you've not got a sub then it'll includes the LFE channel on any speakers defined as "large", thus supposedly risking your speakers.
So what is the practical effect of losing this LFE channel? that varies from film to film. the LFE channel is as it says, an "effects" channel. The content there should also be on the main channels in some form but you may lose some ultra low slam. The reason I say "may" is because the 5 main channels are all full frequency. a mixing engineer can and sometimes do choose not make use of an LFE channel at all and put it all in the 5 channels, in which case, you'll lose nothing. More commonly though, you'll still hear the explosion and get all the details, but it won't rock the room as it would have done with an AV receiver which can control the downmix process.
Interestingly, you don't get this problem on the Arcam SR250 stereo amp because although it is only a 2 channel device, it has a dolby and dts decoder built in and dedicated connections for subwoofers, (and room correction as it happens) so it can control the downmix process and make sure you keep all the slam.
Hope this helps a bit.