I still wonder if it's a good thing for us.
I mean surely it'll add to the cost as either company will want to make that money back as they're both business and in it for the profit. From their point of view I'm surely they can increase prices a bit, explain that it's got an improved cooler and then make even more money. So I get why they doing it.
I'm sure they board partners aren't overly thrilled at the idea that the stock coolers will be better so they'll have to put lower numbers on their marketing (10dB quieter instead of 20dB or -6ºC cooler instead of -15ºC).
But why would you buy a reference board?
- You plan to watercool and so don't want to pay more than you have to for the cooler.
- You plan to run multiple cards and the blower design is best. What you want is a blower design cooler, not a reference cooler specifically (e.g. HIS IceQ)
- You can't wait a month or 2 for the custom cooled cards.
- You're pushing your budget and want the best card you can afford.
So for 1) this just raises the cost of the card.
For 2) generally reference is the only option for blower coolers, but if there were other options (HIS IceQ) then you might go for that anyway, so this makes little difference. Trouble being the lack of custom blower coolers.
For 3), guess there's not much that can be done for people like us

For 4), well they might increase the price meaning reference is now out of reach. And looking at prices now, some of the custom cooled cards aren't that much more than reference (for AMD at least).