... And another thing to note are the file sizes:
- /System/Library/CoreServices/ScopedBookmarkAgent: 78 528 byte;
- /System/Library/LaunchAgents/com.apple.scopedbookmarkagent.xpc.plist: 486 byte.
These sizes are identical on the newly built 10.7.4 system (with the supplemental update) and on the other, upgraded systems (without the supplemental update, where those files were already present): so, probably, they are also the exactly same versions, even if the creation and modification dates are obviously different for those from the supplemental update.
[Edit:] OK, I just browsed through the whole Time Machine history on my MacBook Pro, which was originally built with 10.7.3: and the two files in question were always present, and right from the beginning!
So, it really looks like the explanation for all this is quite simple: they just forgot to include the two files in the 10.7.4 Mac App Store installer/DMG, while they were indeed present in the 10.7.3 one (and the updaters, both delta and combo, also seem to have nothing to do with this).
That might explain why only computers originally built with 10.7.4 get the supplemental update...