Yup, we are making progress (see my edit)... I think the last issue of eARC could be causing the problem?
The Amp Assign and Speaker Configuration are now ok so it could well be the TV and/or the source that's the issue.
Someone else will need to help with your source (NAS) as I've never used one.
Even if you don't get Atmos the Denon will still upmix to all your speakers when you select Dolby + DDSur.
Hopefully a setting or a workaround can be found so you do get Atmos working.