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I don't know about Framemaker, but this is a piece of cake with Word. I did exactly what you describe for four very similar books (two bus interfaces on each of two platforms) over a decade ago.
I didn't have to break the info into separate files, either, because the differences were at a *very* fine level of granularity. We used variables (like "productName" and "versionNumber") and conditional text ("if OS = 'Windows' insert '\' else if OS = 'Unix' insert '/'") throughout the text; I'd just set a couple of control variables at the beginning of the document and update all fields for a new version of the book.
It was the only way I could maintain four versions of each of the two huge manuals that went out with every (frequent!) release.
If your variable chunks run to multiple paragraphs, you can put them into separate files.
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