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