For me as a player, some forms of "manipulation" are more congenial than others. Cunningly designed artificial contours, if done properly, can offer a more pleasing golf experience than a dead-flat piece of property would provide without the shaping. Those courses with frilly bunkers that are carefully manicured to always look just the right amount of "unkempt" can be beautiful AND playable although they would probably be neither if left to nature.
On the subject of trees, in heavily forested property even clearing out undergrowth to make balls easier to find or moving the tree lines well away from greens and fairways to provide light and air movement can be a "manipulation" in what was basically woodland before the course was built. But that "manipulation" is a darned sight better than the alternative (again from this golfer's perspective).
As I mentioned in an earlier reply, the part that beggars belief is that anyone who plays a course regularly might consider fans around the greens as anything but the least-desirable, last-resort, bottom of the list of acceptable "manipulations". By comparison, tree removal, higher cuts, slower speeds, almost any alternative would seem less injurious to the experience of playing the course. I love putting, it is one of my favorite elements of the game. And I love putting on fast and smooth greens. But damn, not if it means putting with those fans roaring all around me on hot days. Give me a smooth but slower green and no fans 100 times out of 100!
It sounds uncharitable but I can only come up with two possible explanations. Either the members of these clubs value the putting part of the game to the virtual exclusion of all other elements of enjoyment or they are totally in the thrall of what they believe is a competition for the absolute highest putting speeds at all costs.