Spoke to Naim technical support today and got an answer for a couple of things mentioned above.
Regarding the standby switch on the rear of the units, it can be switched from auto standby to instant on while the unit is powered on, however switching from instant on to auto standby requires a power cycle. So that rules out @robert_h’s suggestion earlier 
The issue regarding the AV bypass does sound like an oversight and he will raise it internally. However it may need to be a dealer upgrade thing if they warrant it important enough. It is to me.
On the question about disconnecting from the mains when using instant on, seems like pulling the plug (even though they’re fully powered and the manual says to avoid doing that) is the way to do it, in the order of power amp, pre amp, pre amp power supply, source, source power supply and reverse for reconnecting. So same as the Classic boxes.
In our phone conversation he didn’t sound to be completely sure so I’ve asked for confirmation by email.
It would be nice if we could get a reply like the following for the 300 series as they appear to be different.
I had hoped before reading the manual that the New Classic boxes would work in the same way