I imagine some pretty whacked out ideas emerge during early script development of any film. That's why they have re-writes - to produce a script for a film which a mainstream audience will accept - and it's that audience, as much as, if not more than the die hard fans which the film will seek to attract.
Wasn't there a rumour before QoS that a story idea was Bond or Vesper having a child? And yet by the time the finished product arrives, there isn't a trace, even a moment, when you could say "Oh, that took a right turn there instead of a left."
Scripts go through a multitude of drafts, rewrites, adjustments, and one thing for sure is that three different sets of eyes (counting P&W as one joint set!!!) have been on Spectre with explicit instructions to add/subtract. And looking at the specific strengths and order of involvement of the writers, there's a clear logic as to how things could have gone:
Logan - 1st draft, pitching original idea. Probably not too many limitations - free hand to establish an idea. Could all stay, could all get binned (see Peter Morgan, or the legions of writers that worked on TSWLM or TND, to name two films. Anthony Burgess, anyone???)
P&W - next up, explicit instructions to "Fleming-ize". Makes sense, the team know their source material (very well, IMHO, and something that I'm not sure we have always given them credit for), and they also know EON's relationship with the character and the source material (a fascinating discussion that we've had over the years).
Jez Butterworth - knows Mendes, established playwright/screenwriter, punching up and dialing down where necessary to put the final arranging in place (similar to Haggis on CR perhaps?).
Speculation on my part? Of course. But to me, at least, it does speak to some quality control (not to mention the input of the director, producers, and the lead,) as to what will eventually end up on screen.
I'd be a lot more concerned if Bond was in any way an "auteur" product. But it's not. Mendes is now on his second Bond - he knows how this particular production company work. If this was his first film with EON then maybe you could voice a concern that "this guy with his artistic trappings doesn't get Bond" but I don't see that argument flying, not after SF.
To be honest, I'd love to know the authors of those e-mails - if it was the usual studio stooges then I might be worried. Some of the rubbish down at the cinema has me questioning those that make big money at the studios these days! As for EON, they know what they're doing, and more importantly, there know full well the product that they "own."