So the DPAD on your Samsung remote doesn't control movement on your Apple TV?
Well, it all magically started working. I had to disable and re-enable several times on both Apple TV and Samsung tv and it just started magically working.
I still have not figured out how to get the Apple TV to go to sleep when I power off the Sony TV with the Sony remote. The All for One Streamer does this, so I'm guessing that its sending something to both the TV and Apple TV to make that happen, or sending to just the Apple TV and the Sony's CEC is turning it off. What I have noticed is that every once in a while I find the TV off and the Apple TV asleep when I didn't turn it off. It is usually when Channels DVR has a show paused I think, but need to pay more attention. When I hit power, the TV comes on and Apple TV wakes right up. So not sure what is triggering that, but it gives me hope of fixing it.
In the mean time, I've been able to program the One for All to do a few more things... Guide to the red power button, Live to the * button, Channels up/down, and the Back button for last channel. This is close to good stuff now. What I can't figure out how to do is program the 4 channel function keys. The documentation and their tech support person say they can learn a key from another remote; but I can't get that to work. They an be taught macros, but only from the keys that are already programmed on the remote which doesn't help me with the colored function keys on the Sony remote.
Did you manage to resolve this? I’m having the same issue. Tried deleting things and starting again, but still no joy.
Open the Harmony app on your phone, go to Devices > Windows Computer and click one of the dpad keys. It should walk you through the pairing process.
Yeah that was my problem too initially, but only with the Elite. In the activity for your Apple TV I had to make sure the connectivity was set to the Windows device and not the Harmony Pro BT Apple TV 4.
Thanks both, managed to get this working eventually with your tips. Seems like it couldn't be connected to both the "Harmony Pro BT Apple TV 4" and the "Windows Computer" at the same time. So just added the "Windows Computer" to my old "Apple TV" activity and ensured it was connected to the "Windows Computer". This allowed me to use both "Apple TV" remote commands along with "Windows Computer" ones.
Loving the ability to jump to Recording and Guide!!
All the new features work great on my Sony TV with the Sony remote. Well done.
But my girlfriend prefers the Siri Remote and I can't find a way to control Channel UP and Channel Down with it. Could someone help?
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How would you control channel up/down with a remote (Siri Remote) that has so few buttons?
You said that everything is working from your Sony remote. Are you able to get the Apple TV to go to sleep when you power off the Sony TV with the Sony remote? That is the one thing that has eluded me.
Are you able to get the Apple TV to go to sleep when you power off the Sony TV with the Sony remote? That is the one thing that has eluded me.
Maybe just set the AppleTV to "sleep after 15 minutes" (this is under General settings) as a pretty good workaround?
I am able to do this. However, the Apple TV must NOT be streaming when you turn off the TV. If is is streaming video and/or audio it will not turn off with the TV remote power button. If my apple TV is NOT streaming (at Channels Guide or Apple Home page, etc.) the Sony TV remote WILL turn off ATV4. Of course, HDMI CEC must be enabled on both the Sony TV and ATV4. Also, on Sony TV check: Settings>External inputs>BRAVIA Sync settings>Device auto power off, and make sure it is on/enabled.
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Well you finally solved my mystery. I have been trying to power off when a show is playing, like I’d do with a cable box.
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Yeah with the Elite that's the case for using the actual remote keys (for some weird reason) but you can leave the "Harmony Pro BT Apple TV 4" there in the Activity and then have the activity power it off. This way when you stop the activity with the power button it'll actually turn the Apple TV 4/4K off.
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Went through the process with my harmony hub and Apple TV 4K today. Very nice! Hopefully you will add these instructions to the documentation area you are putting together. I know you’re planning to stick to navigation options only for the colored buttons, but I’ll still put in a plug to add some limited other options as well. Toggle CC being at the top of my list. 
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Glad you got it sorted - I am trying again after giving up. Maybe I am being dim but how do you add a device to an existing activity and how do you change the connectivity from Apple TV to Window PC?
I can create a new activity with all the devices and when it asks for an Activity type selecting Watch PC will connect to the PC but AFAICT this means I get none of the Apple TV button assignments.
Any help appreciated.
To add a device you have to choose “Re-run activity” in the settings for the activity.
As far as the buttons, you have to actually go into “Customize Remote” and set all the buttons that you want. I have everything set to the Apple TV buttons except these for the Windows Bluetooth device on my Elite:
Channel Up = Page Up
Channel Down = Page Down
Record = Record
Guide = F3
Red = F2
Green = F3
Yellow = F4
Blue = F1
Thanks Tim - that helped a lot!
Now trying to figure out if I can map the touchscreen number pad to allow me to go direct to a channel
I'm also trying to map the touchscreen number pad so I can program favourites channel screen in the Watch TV activity.
I haven’t figured that out yet 
Edit: I did below.
So I’m testing 2 activities
One is a generic activity with all the relevant devices added and configured. I can input individual numbers via the touchpad and that works.
The second is a ‘Watch TV’ activity as I was hoping to use the Favorite Channels shortcuts like @nigelsmith . Same devices, same remote customisations but neither the number pad nor the favourites work.
For the Watch TV activity all the buttons were mapped to my TV initially so I am guessing the number commands are also.
It’s frustrating that you can’t program the touchpad in the same way as the physical buttons.