Ignition sequence on 2016 ND not working

Just had a thought and wanted some clarification, do you mean this:
sec05-red
or this:
key03-red
The former is the Security Indicator Light while the latter is the KEY Warning Indication/Warning Light.

From your initial description I thought you meant the latter but I wanted to check. The manual does mention the scenario I believe you are seeing:

If the KEY warning light (red) illuminates, or the push button start indicator light (amber) flashes, this could indicate a problem with the engine starting system. This may prevent the engine from starting or from switching the ignition to ACC or ON.

It then goes on to state:

Have you tried the following:

  1. Disconnect the battery
  2. Confirm the battery has a decent voltage with a multimeter (or battery charger) while disconnected from the car
  3. Reconnect the battery
  4. Retry starting

I have seen mention online of a faulty sensor draining the battery.

And if you have been testing with both keys please ensure there is only ever one actually in the car as it might have a tantrum.

Finally, can you find any other issues that also occur?
So far you have mentioned the infotainment system settings and boot alarm behaviour and I have also seen posts about the interior light.
When this happens, what else doesn’t appear to be functional?
I ask as I had some “fun” with my car where a whole series of different aspects failed but knowing them all I could trace them to a single origin (a certain computer).

And finally, finally, it could be the the starter relay or main fuse causing the issue. Have you checked these?

Thinking about it, I am leaning towards the starter/alternator side of the main fuse having gone.