I agree with nomurine that such ideas are quite possible. Who will understand what goes on in Endo's head?
So many forget this has always been a Sci-fi series. Anya reads minds, Bond can predict the future. Would it be so absurd for the supposed main villain to be an alien?
Well, it was already kind of clear in the first chapters about Anya and Bond that they were "experiments". And this has a lot to do with war stories (people imprisoned to serve as experiments). I don't see much of a problem in either case because, like, it gave the feeling that it had some minimal plausibility.
If Desmond was in fact an alien, as mentioned, the story would be different. And it even explains a bit of Yor and Yuri's "superhumanity" (Yor is kind of "superhuman" in assassination techniques, and both can handle pain and torture well in a certain aspect).
But like, it's kind of hard to think that Spy x Family will change the tone of the story with this. It would be too absurd and people would "skip" the series completely.