Adam,
I'll disagree with you over the term "pedestrian" when it comes to the Links nine...I'm confident that a blind draw of 25 GCA regulars would find 2 of those holes pedestrian at worst, with the other 7 being considered heroic, charming and inspired.
The hand of man...is evident at Merion (dug out of a quarry) Country Club of Buffalo (dug out of a quarry) and many other courses. In fact, the hand of man is seldom absent when it comes to golf. Many choose to don their rose glasses and submit to denial, but golf courses were created by mankind. Topography by nature, golf courses by mankind.
I'm not certain which first green is surrounded on three sides by water...it's not the Quarry nor the Preserve nines, so you must be incorrectly recalling the first at the Links. The 7th green backs up to the first at Links and water hardly comes into play, except as a visual. Remember that there are a road and houses between that green and the lake.
I was blown away by the links nine, as I found it to be a well-designed yet not overly-long half course. With the exception of #9, which is a disaster, the nine gets my vote as top-notch. If there were only some way to incorporate #9 Quarry into the Links and eliminate #9 Links, we'd have a most consistent nine.
If it quacks like a duck, it's probably a duck. If you have a quarry for your golf course, your course is going to look like a links...nope that's not it. Wait for it...a heathland....nope, that's not it...keep waiting...A QUARRY COURSE !!!!!! Honestly, it's inane to suggest or expect otherwise. It's a fair run of holes with two natural par threes (don't forget the 8th hole, the one that runs down to the lake) and a bunch of others. Unlike #9 Links, there isn't a hole that far-fetched, although #6 comes close. The fairways are wide, the greens are large enough to receive a variety of shots and the course plays as a memorable resort course.
Since I didn't get around the Preserve, it very well might wreak of forced, inconceivable negotiations. I'll reserve judgment until I return to Petoskey.