Software teams still measure in man-months. We just call them something else, like "story points". I've never seen any estimate or schedule which included team communications costs.
Second-system effect is still just as common as it ever was. We still fix bugs, and in doing so, create other bugs. Many or most systems lack conceptual integrity. We still hire implementors before the architecture is finalized.
I've seen pilot systems only very rarely. I've never seen an architect produce a manual of specifications. I've never seen a surgical team, or anything even vaguely resembling it. I've never seen tool-maker as a dedicated position, even when my manager agreed it would be useful to the team (on the basis that "nobody would want to take that job" even though I volunteered).
The only piece of TMMM that I've ever seen or heard any team try to apply is "No Silver Bullet", and that only as a catch-phrase used to mean "we're fucked either way so don't try". Nobody quoting Brooks has bothered to read that chapter (or that paper) and find out Brooks's criteria for what would constitute a "silver bullet", or try to make one. I can think of a couple examples of partial attempts, but always by UI/PL researchers, never by software engineers quoting Brooks.
Are you looking for "the book everybody knows they should read but nobody actually does"?