Hi guys,
First, you should be able to get both the internal GPU and a PCI-E one working together. They do on my Gigabyte MBs. On those, though, you have to manually enable it in the BIOS. "Auto" mode disables the internal GPU if an external one is present. Probably the wrong thing to do these days; On my box, with an Ivy Bridge CPU, TMT doesn't work at all unless the internal GPU is enabled.
Over the years I have used both fanless and fanned GPUs. I started out with a fanless Nvidia 7600GT, then had fanned ATI 3850 and 5750 and now have gone back to fanless with my Sapphire 7750 Ultimate. In the past there has been some debate whether a fanless card was always even quieter, since a fanless card needs some airflow inside the case to work and sometimes, what noise you lost from going fanless could be regained by the need to increase case fan speed. I'm sure you know fans typically make very little noise at low speed, but a lot when they get close to full speed.
GPU fans can be very quiet at low speed. The fan on my 5750 was just about silent playing hardware accelerated video over the then noise of my old c2d system, which had a relatively noisy processor fan and needed quite a bit of case fan action too. It was not so quiet gaming or using MadVR. When I moved to Ivy Bridge, which runs a lot cooler anyway and which I added a good CPU cooler to and so is virtually silent outside of my AV cabinet, I decided to go for a fanless GPU again. I am sure I would have been really annoyed by my 5750 using MadVR in this setup.
The AMD 7750 runs so amazingly cool I strongly recommend it, but of course it depends on your budget and I haven't tried all the others you were looking at. I would not go for the 5450 and possibly not the 6450 either if you want to use MadVR in all its glory. MadVR is more like a game in the way it drives the GPU.
Lastly, just tried jinc 8-tap on my 7750 and NO WAY IT COPES!! Boy is that punishing - about 90ms rendering time for 720p upscaled to 1080p! 4-tap is fine though. I'm not sure the 6970 in my gaming system could do 8-tap! But, from everything I have read in Madshi's thread I am not sure increasing taps really benefits jinc in the same way as lanczos. I think I will be very happy with 4 or even 3 tap.