In a presentation many years ago, someone asked me under what circumstances I might be comfortable in telling a difficult client "no." I cracked a joke about it being the day my last child graduated college. Someone just reminded me of that line, some 20 years later.
More seriously, having worked with some dogmatic PGA pros (and owners) I usually accommodate where reasonable, and tell that they should trust me to prevent them from implementing any "lay the green side of sod down" type directives. Not sure about the greens on the dunes, but if it was illegal, I would probably protest, and then follow up with a field report that I did in fact recommend strongly that move not be made, knowing guys like Trump usually, but not always, get a pass on stuff like that.
You would be surprised (perhaps) at the number of illegal directives we get, usually to skirt environmental or ADA requirements.
I had a similar situation when designing a course on an island in the middle of the Yang Ze River a few years ago. I had routed the second half of a par 4 up the hill away from the water to shorten the walk to the next tee, but the client asked why not on the river, since carts would be required. It also causes an unsafe walk back, etc. but I changed the plans, seeing why he thought it was better. And, the course will most likely never get built anyway.....