"The Big Bad Thing has so many manifestations that it feels like monster of the week rather than a true full book that holds onto a core sharply executed identity."

This is one of the structural weaknesses in the entire SCP... motif, for lack of a better word. When a core part of the premise is "you can't understand it, not even in principle, if you think you understand it you're wrong", the premise does some fairly fundamental damage to what most people would consider the basic structure of a story. Generally we think that at least in hindsight, a story should "make sense", but SCPs by their nature have to be somewhat random and lack predictability or they aren't SCPs. You can try to wrap a more conventional story around that particular motif, but you've always got this fundamental structural weakness sitting right smack in the middle of it, and you can't remove it without leaving the sub-genre. The SCP structure fundamentally starts with a negation of this aspect of stories.

It is fun seeing what some people do with this limitation, and there are after all compensating benefits or nobody would write in the universe. But it is something that is going to be there in any story set in an SCP or SCP-like universe.

I think it was Larry Niven that observed that most stories are judged by something like character, plot, theme, etc., and that one of the distinguishing characteristics of science fiction is that you have to add the background to the list of things to look at. But only a vanishingly small set of works ever managed to have character, plot, theme, and the other characteristics firing on all cylinders as it was; asking for a work to have all that and also be 5 out of 5 on the new setting it establishes as well is way too much to ask of a work. With this sort of story, as a reader you are putting all your chips on the setting. Going in to this sort of work you should expect the conventional measures of a story to at least take a hit, and in many cases a fairly large one. And of course, if that's not what you want, then you're not going to enjoy it and I have no problem with that. This is less a "defense" than an explanation, that if you didn't particularly enjoy this, I'd suggest staying away from the entire subgenre because the entire SCP subgenre is structurally prone to these issues from the very foundation on up.

(To give another example, Greg Egan has a number of works in which he fiddles with the laws of physics, to do things like have two time dimensions and two spatial dimensions, then works out how that actually affects physics using math rather than intuition and write stories in the resulting universes. This is such an investment into the setting that I don't find it all that surprising that I don't find the characters all that compelling per se. There just isn't the room. But you can't get that setting anywhere else.)

Sci-Fi Short Film “There Is No Antimemetics Division” [video]