OP, you hold an underlying assumption here that I doubt is true. You believe that any PWM fan is going to be significantly quieter than the fans already installed on the graphics card. Why?
There are lots of posts and stories around that talk about older-style 3- pin fans being 'way too noisy because they cannot be speed controlled. Almost all of them are based on false info. It is true that the speed of a 3-pin fan can NOT be controlled by a fan header that is using the newer PWM Mode to control its fan. BUT if you change the header's configuration to use the older Voltage Control Mode (aka DC Mode) it CAN exercise proper control. I am SURE that, whichever fan type is included on the graphics card you are buying, its design INCLUDES ALREADY the proper type of speed control Mode, and that card WILL automatically control its fans' speeds according to its temperatures.
If you want to see the LACK of difference due to motor type, look up fan makers who sell matching fans with either 3-pin or 4-pin motors. A good example is Noctua. There you will find many cases of fans of the same design that produce identical fan speed, air flow, backpressure and noise ratings but differ only in the type of motor used.
Now, there ARE differences among fans in air flow, backpressure and noise generation that are rooted in the fan design, and NOT in the type of motor used. So it is possible that you could find some PWM-type fans that generate the airflow you need against the backpressure imposed by the heatsinks on that card, and still generate less noise than the stock fans. To do that, FIRST you need the exact specs of the stock fans you propose to replace. THEN you have a basis for searching out alternatives with matching performance AND less noise generation. Unless you can do that, you have no assurance that your plan will work.
You should be aware of another factor. I don;t know what type of fans are already on that graphics card. IF htye are 4-pin PWM-type fans, why would you make the change? But IF they are 3-pin fans, I have no doubt the fan control system built into the graphics card will be by Voltage Control Mode, and cannot be changed. So even though you change to PWM type fans, the actual control of them will be by the older Mode, which CAN work but is not as good as proper PWM Mode for those fans, and basically eliminates the advantage you seek.
Now, I can see that you plan insterad to have the a mobo header that uses proper PWM Mode to control the new fans you propose to install. BUT that also means you have ASSUMED that your graphics card does send out its temperatire control signal on a contact of the card's PCIe slot so that software can access that info and use it to direct a mobo header. Many cards do that, and the utilities that come with the card can read the temperature info and show it to you. But whether or not any third-part software can then access that info and use it is another assumption you would need to verify before proceeding.
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