If you'll look in the Assembly Manual, if a part number is shown for a particular bracket attaching bolt where an engine plant bolt was originally installed, that means the engine plant-installed (orange) bolt was removed and replaced with a new one. If no part number is shown for the bolt or the illustration says "part of engine assembly", that means the engine plant-installed bolt was removed and re-used.
For the specific application in the first post (rear A/C compressor bracket to intake), a part number is shown for those two bolts, so the engine plant intake bolts were removed, trashed, and replaced with (longer) new bolts.