Is this really a big deal?
The sound of the fan is somewhat annoying but reasonable when you consider the GPU is pushing four times the pixels.
The throttling seems very rare. I've not experienced it when gaming and most posters on this thread haven't hit 107 degrees.
And if the heat does damage the components then everyone has a minimum of one year's warranty. If the components were going to fail due to heat alone I'm sure it'll fail in a year or less.
I'm sure Apple engineers know enough of what they're doing to know what temps their GPUs hit and if it's safe.
No-one knows for sure yet. Potentially, it is.
That said, it sounds like it wouldn't really bother you if it was, and you are happy with your product. If that's the case, just enjoy it!
How do you know you've not experienced throttling? If you're running a game at 100 FPS. When it throttles, it will only drop to 90 or so. As a human, you're unlikely to notice that. You need to measure the clock speed/FPS to see it.
So then you could argue, "so if you can't notice it, who cares". That's fine, if that's your view then the 5K iMac is perfect for you. For me, though, I don't appreciate paying for something I don't get. I paid for that GPU, and I get to use its power for about 60 seconds. In a year or two, that missing performance will be needed more and more. Not cool.
I have managed to get my M295X to 108C on Windows without really trying, and 106C on Mac. The temperatures are consistently maintained and fall outside of the operating temperature of the card. Consistently running electronics outside of the safe temperature, at least in the past, has not led to positive things.
Sure, I could keep it, let it fail and use my AppleCare to get components replaced. But besides the hassle, that doesn't solve the problem. I will still hit 95-100C and hear the fans when watching some 1080p movies, I will still be throttled when doing any intensive task, I still won't be getting the advertised performance. The 2013 iMac is outperforming it in this case. I'm not happy with that.
Looking at the lawsuits and failing AMD cards in the 2011 iMac/MBP suggests otherwise, with regards to your comment about Apple engineers.
When I bought the iMac I said to myself, "anything short of perfect, and it's going back". My returning of it is me keeping that promise, nothing more.