Not an invalid comparison at all... I'm comparing two 12mp images (apples to apples)
You're not.
What you are comparing is 12 mpxl images which were derived in different ways, one of the ways giving one image an unfair advantage over the other by masking the faults in it's recording process. See our digitisation equipment does not detect colour. Both your scanner and your camera record only the lightness of each individual point, but they do so through a red green and blue filter. These filters then are used to derive a colour picture where each pixel is made up of a red green and blue value.
Film does not work like this. Any given point on the medium has a full colour range as that point can be dyed with any combination of dyes. Your digital camera on the other hand has 3 million blue pixels, 3 million red pixels, and 6 million green pixels. Interpolation is then used to derive 12 million full colour pixels, it's not perfect but it actually works quite well. This however relies on any given point source of light falling across a group of 4 pixels in order to derive colour, which is done by a layer of bifringent glass on the sensor called the Anti-Aliasing filter (or low pass filter since it has a coating that also blocks IR). Effectively for a sensor to work you need to blur the image then sharpen it.
This is true of scanners too yet their implementation differs. Where you're falling short in your fruity comparison is that by resizing the picture that was recorded you effectively sharpen these slight nuances, much the same as reducing a 12 mpxl DSLR to a 4 mpxl DSLR effectively doubles its sharpness.
But it's not only the film itself that you're now putting at an advantage, but also the recording system. Medium format has larger glass physically and thus very different lens characteristics such as less diffraction. By downsampling the image or scanning it only at 12 mpxl you're also giving the lens on your medium format camera an unfair advantage over the film lens.
Either way you're never going to have an apples to apples comparison of film vs digital. Although you could get close by comparing a film shot by cropping the appropriate area, scanning at high resolution, and rescaling it to be the same sized as an image from a camera equipped with a foveon sensor, using the same lens.