I guess anyone who spends so much money expects the best quality and doesn't want to risk with a brand that has a history of mediocre products or saves $3 on a cooler. If a reference design was available from all brands, like it was some years ago, then we could pick any brand and expect similar results. However, right now, the reference design pretty much comes only from Nvidia. There is something behind the final price of custom designs, and it includes everything from the product itself to added services. Nvidia FE cards often cost more than custom designs, and there is also reason for that.
I'm not sure who started it, but EVGA was one of the first brands to use warranty stickers that only let support know to examine the PCB for mechanical damages. ASUS, Gigabyte, and MSI introduced that later as the EU laws forced them to do that - the product couldn't have a limited warranty because of stickers that can break for various reasons. Before, there were even cases when some brands damaged stickers and said the user did that. Somehow, brands like Palit still use stickers that clearly state that you will lose the product warranty if you remove them. They even put it on some special OC series - not only a cooler, but also a switch unlocking higher capabilities had the sticker. If you wanted to push the card, your card was without a warranty.
I'm not sure if we are talking about the fan/OC software, as MSI and EVGA used to have the same software based on Riva Tuner with changed graphics, so it's weird to hear that MSI has the best software and EVGA has the worst

I agree that Palit has very bad software. Users often mentioned that some options don't work. Gigabyte software was always annoying for me - a lot of stuff, not everything works, and with RGB around, they run 5+ services in the background. The same for ASUS, but ASUS soft once fully updated, at least works.
Coil whine is sadly hard to predict. Even cards with the same product number have it more or less audible. I remember some users were getting card replacements for that and later said it was much better. This is an even worse issue than with fans, and when you are unlucky, then it's louder and more annoying than fans at max speed. I couldn't stand with my old Galax HoF card, and I sold it. It was literally causing my head to hurt after 1h in 3D.