I apologize if I missed anything while reading this thread but it seems to me that your main issue here is your Bitfenix Prodigy which is a "tiny" case with not much airflow. You installed a open air cooler video card in here, which by design, needs the case to do the work to remove the heat properly(as opposed to a blower type cooler which is what you usually want to use in a micro ITX case).
Glad you pointed out all that. You're quite right, the Bitfenix Prodigy is quite tiny, but looking at cases released in recent years, this little case has some merits but not robust. The hanger attached to the base of the case has broken 6 months ago. I have to use some unused books to elevate it. When you mention blower type, I suppose you mean front intake and exhaust at the rear?
Most reviewers will use an open benchmark table for their test which means that they don't have to worry about poor airflow to their components or heat buildup inside of the case so the numbers you'll find will always be on the lower side of things compared to a normal setup. They also usually test with a controlled ambiant temperature. You're posting this in summer(assuming you live in the northern emisphere) which means that, depending if you have AC and how heavily you are using it, you could be also adding a few degree to your temperature readings simply because of that.
Thanks for the information. I do have the same feeling too. Indeed, if I get the air conditioner on, the card's temp drops by 3 degrees. This ASUS card is very sensitive to ambient temperature.
I'm not saying that this card wouldn't perform "normally" and be "cool" in a case with great airflow but that's the first thing I would look at considering you are currently speaking about upgrading said system.
Several reasons really, take a look, I have taken a screen shot while I was replacing the rear stock fan with EK Furious Vadar FF5-120 3000 RPM Fan just purchased from a retailer downtown. My beloved ASUS P8Z77-I Deluxe was dusted heavily around the CPU area (sorry for the poor quality I used one of my very low end phones)

Another reason is that I ve found my new graphics card very fast, 173% faster than my previous GTX 560 Ti.
https://gpu.userbenchmark.com/Compare/Nvidia-GTX-560-Ti-vs-AMD-RX-570/2180vs3924 In fact, it runs Mafia II, Civilization VI, Assassin Creed Syndicate, all above 100+ and lately I have got Railway Empire which runs 60+ FPS. I naturally presume that upgrading the CPU will certainly further increase all games FPS and secure a better FPS performance for future games when they are optimised for more cores and threads.[/QUOTE]
PS:My post is written assuming you are using the Bitfenix Prodigy as it came out of the box and that you didn't add more fans or modify it. I also assumed you were using one of the models that didn't come with the open mesh type panel on the front(the black one, all or the others have a solid panel blocking most of the airflow).
Your Sherlock Holmes style stuns me! You're right I have never change the stock fans and default orientations which I regret very much. That's why I have purchased the 3000 rmp fan. I have also attached the image of the stock Bitfenix fan.
To be fair, the Bitfenix fan is very very quite, whereas this new Furious Vadar has it name chosen most appropriately, when it is operating at 50% I can actually hear the bearing sound (unlucky probably, got a bad one from the retail). I am learning to use the SpeedFan and tried 100%, it sounds a little like a vacuum cleaner to be honest. Having said that, I can feel with my hand at the rear of the case that air are pulling out obviously, compared to the 3 pin stock fan. I also removed the front mesh panel (see my screenshots). I thought this will help ventilate more air intake at the front and let the Furious fan furiously pull all the air out.
But I am not sure if I have done one thing correct, see the screenshot, I placed the Corsair 120mm radiator/stock fan at one of the fan cutouts. Now as I have the other stock fan idle, shall I install it to the remaining cutout and should it be pulling out air or pulling air in? Both the radiator fan and the other fan are 3 pin so no control of their speed is possible.
By the way, It's really a comfort to have your replies, I have been coming back a couple of times but seeing there were no replies I left...