The reason for using a big bolt to plug the existing holes is so the threaded holes don't overlap. The original stud hole is drilled oversize and tapped for a 5/8" diameter bolt. Then a bolt is threaded in, cut off flush, and a stud hole is drilled and tapped in each plug at a closer spacing. I used to use a similar procedure when moving the rocker arm studs away from the valve stems to get the proper geometry for small block Chevy racing cylinder heads when changing to different-ratio rockers. If you're planning to go back to the original stud spacing at some time, having the manifold plugged with a large-diameter bolt would also be a good idea since the plug could be removed and another one installed, threaded on center again for the wider stud spacing.
Jerry

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