Looking at the "listing" or the various reason for St Andrews Links to be given this status, it all appears to be about the history of the site as a whole, including the other courses, and how it has been used for golf by the public over the centuries. It also refers to its setting, with the holes being very much part of the town.
It doesn't however mention anything along the lines of "excellent and original examples of strategic golf holes" or "notable for its fine examples of bunker placement and styling " or "the 17th and its road hole bunker are particularly fine examples of golf holes". However, a listed or protected building may have within its listing such phrases as "fine and rare example of medieval stonework" or "excellent example of Georgian windows" or "a fine example of early English modernism" and its these specific descriptions that help to make it clear what is to be protected and to help inform any future adjustments.
Therefore, the way I'm reading it is that as long as the links as a whole remains as such, I can't see Historic Scotland being too concerned?
Perhaps it's only us GCA geeks who are so concerned with the actual architectural content of the old course and unless the golf course architecture itself can be listed, as discussed on the current thread started by Tom Doak, then such adjustments aren't going to be an issue for the wider public and golfing public as a whole?
Cheers,
James