Enysse, lots of questions. First, if I said or implied that legal and ethical were the same thing, I apologize. I don't think I said that, but I want to be clear, they are not the same thing.
Now, we don't know if what you describe is what's happened here, at least not from the thread. But let's assume it has. There are lots of ways to "breed" animals. You can keep deer in a pen, and make sure of the breeding, or you can keep a big buck alive in a high fenced area and let nature take its course. As for the food, you can feed deer in that small pen, or you can create food plots and supplement the food plots with minerals. Both seem to be common practice in many parts of the US, as I see on shows like Realtree Roadtrips, or Bone Collector. How about "culling" "management bucks" to get the smaller ones out of the gene pool? I'd say in all cases the deer was "genetically bred to have horns that size and fed high protein and babied until it was shot". And in both cases nature was helped along, a bit more directly in the pen maybe, but I'm not sure the pen or the high fenced ranch makes all that much difference. I don't much care for either, but I won't fault it so far on ethical ground, so long as it's legal (it isn't where I live).
Now comes the harder part. You ask if I'm Ok with selling a particular deer to a hunter who has enough money in a 1000 acres enclosure. First, selling the deer. I'm OK with selling the right to hunt deer on a particular property. That's done throughout the US, and again, it's legal (and again, it's not legal where I live). So far, I don't have a big ethical issue. As far as the money goes, well, the fellow who bought the black rhino permit in Dallas has a bucket load more money than I do, and I don't begrudge him doing what he wants with it. Elephant are expensive too, and I wish I could hunt them all the time, but I can't. But I'm not saying that anyone who has the ability to do that is wrong. So the money doesn't enter into it in my view.
But now we get to the hard part of your question. If a deer is taken from a pen, and put in a particular area, to be shot by someone who has picked that particular deer out of a lineup, then even if it's legal, I have an ethical problem with it. But what if the "pen" is 50,000 acres, like some of the ranches in South Africa are? Now we're speculating, because in an area that size, you might never find the deer again (at least not on a 10 day safari), so no one would do that. But if the "pen" is 1,000 acres, and the deer has no realistic chance of getting away, then I would say even if it's legal, it's unethical. And frankly how it's been bred really isn't relevant.
The "pen" part is what's not good for hunting in my view, but again, we need to be careful here. All of the hunting shows that have sprung up over the last few years on OLN or Wild TV here in Canada seem to be having the effect of increasing the number of hunters, and maybe even to some extent increasing the acceptability of hunting. And lots of them look like "pen" hunting to me.
At the risk of really setting off a war, I can tell you I have way more problems with places that feed (which is to say, bait) "wild" deer, supplement the feed with minerals to maximize horn size (calling that a "quality deer management program"), set up game cams to pattern the big bucks, and once you know where they are and where they go, and what time they go there, put up a tree stand and sit in it and wait as long as it takes for that right buck to come along, and then take it a 10 or 20 yards.
So to finally answer your question, and apologies for the length, I don't accept "pen" shooting because I think it's unethical (and we can argue about what constitutes a "pen"). But I guess I just don't see the difference between breeding deer in a pen and breeding deer on a ranch. One is just a bit more controlled that the other.
Now if you want to get into breeding for things that don't occur in nature . . .well, that's probably a topic for another thread, but I will say I think it's both unethical, and bad for hunting, regardless of how the animal is shot.