Until FindMyPast admit that, contrary to their publicity blurb, everyone living in England and Wales in 1939 was NOT included on this register and that they need to look into where these missng people's details were kept as and when they were issued with ID cards etc, we're not going to make any further progress.
It is quite a big jump from not being able to find them to saying not everyone was included in the register. As they needed to be on the register for ID cards and rationing purposes, I would say it's extremely likely that most people we currently cannot find are indeed in there somewhere. Probably a lot less people are ACTUALLY missing than in, say, the census.
In defence of FindMyPast, they don't know you, they don't know how thorough you are with your searching. I'm sure there are people out there who, if something isn't EXACTLY where they expect to find it, swear it is missing (I am not for one moment saying that is you), and the job of that e-mail is to "encourage" people to think outside the box.
However, I'm equally sure there are many, many instances of people being missing from FMPs indexes of the register or mistranscribed. With something of this size, I suppose is almost inevitable.It happens on all similar releases (Anc's Electoral Rolls for London were - still are - a nightmare). What makes this harder is that we cannot currently see everything. So when we say to FindMyPast "something is missing", it is so easy for them to reply that it is just us looking in the wrong place
You're obviously a much nicer, more forgiving person than I am, ReadyDale.

If it was just an odd person here and there that I couldn't find, I might be convinced. However, both sets of grandparents are not be found and neither are the addresses where I'd expect to find them. I searched for my grandmothers separately in case my grandfathers had gone off to fight (despite their ages and that they'd already fought the Hun in 1914-18) but still no sign of any of them. Then, thinks I, perhaps one of them is with her other family - look for older sister, nothing. Look for in laws - nothing!!
You can see why I'm not very happy with FindMyPast? I'm not saying I'm brilliant at these searches - far from it - but I have been doing this well over 10 years now and I do know about mistranscriptions but not to find
any of the above is rather a coincidence. The main names (Russell and Gibson) are not that easy to mistranscribe, though I did find a great uncle and aunt transcribed as James & Emily Rumble, which I quite fancied and considered changing my name by deedpoll.

One name I've been looking for - Stubbs - is notorious for outlandish mistranscriptions, but, amazingly, seems intact in the 1939 Register!!
As you can tell, I'm starting to go ever so slightly bananas over this....