Brian,
Not often, but it does happen.
At the Quarry at Giant's Ridge, I helped them select among four sites. Things like the need for a different look and more importantly, ease of utility connection led us to the Quarry.
At Fortune Bay, we were allowed to choose from two sides of the reservation.
At Woodland Hills in Nebraska, the owners farm had some potential to morph a bit into another farm, and we changed that routing mid stream to take advantage of cerrtain features. Similarly, the City of Lincoln had more property than we needed for Highlands GC, and we had to decide which part of the property to put it.
But, Giants Ridge Quarry is the only time I can recall (out of 45 courses designed) that I actually got to pick a site......