well yeah, IF there were not MULTIPLE blast doors between the active portions of the mansion and teh "forgotten caverns"
but as the name implies, it is highly likely they sealed off those zones long ago, and "forgot" about them being behind blast doors for "security"
can a blast door mixed with the sheer amount of noise some of the shit ramoray and company would be doing actually not drown out a far-away blast behind multiple blast doors?
I suspect that the map is inaccurate in terms of relative distances, I mean your house is compared to other blocks and you were told you have "several hundred acres" and would the mayor live on less than 100 acres? and what about hiding elsa's house? I suspect the map is basically a zone of several dozen miles in each direction, not just a few city blocks
this fixes the "nearby" flaw and the "shockwave" flaw and even the "noise" flaw of the raid, if you hear a boom muffled by several dozen blast doors, several miles distance, and covered up by local noise, you are unlikely to know what happened, especially if clacks and bangs are part of the local noise floor(very likely in the lab and assuming the vast underground transit system for such a town-wide tunnel system)
but yes, the rest of it is very normal for even a real-world version of the organization(discounting the medical bullshittery) such a story could legitimately happen, and if we did have an "RA-63" they would have a type of "narcan" for it and maybe not a full cure(likely designed by the boss to be ONLY a lifesaving measure and forbidden to make it better), such a treatment may save some women but others may be brain-damaged from the events(they do reference the pituitary gland as part of the cure path, making it likely it is just something akin to anti-depressants and depressant drugs that just target the rational brain's ability to have self-control)
but all in all I want this VN to reach at least 20 chapters of similar length, the idea of maybe even seeing your kids take over and possibly ruin what you did would be just as interesting