How sure are you that the GFX 100 sensor is only ~$1000? There has historically been a size point where sensors become much more complex to manufacture, because they can't be imaged on the wafer in a single exposure. It had been under 24x36mm (I presume that's been fixed, since full-frame cameras have dropped so radically in cost) for many years. Years ago, Canon's APS-H sensor size was a response to this - it was the biggest sensor they could make without stitching on the wafer. Since there are now $1300 24x36mm cameras using current generation sensors, I'm guessing that those are easy to manufacture now.
I don't think medium-format sensors are single exposures? Of course the 50 MP sensor would have the same problem - but Sony could be selling through existing stocks of those (at a discounted price, because they recognize that they have to compete with the highest-end 24x36mm sensors) or they could be made on an older line that can't be switched to manufacturing the 100 MP sensor (or another newer sensor with a better margin per wafer). If it's made on an old line that has few other products, it's worth making as long as it covers the costs of the wafers and keeping the line running - while the 100 MP sensor has to compete with making many more, smaller sensors on the same machines.
For these and other reasons (I don't know about others since I'm not a chip designer), I could see the 100 MP sensor being several times as expensive as the 50 MP. Sony could also simply charge a much higher margin on the 100 MP part, because they know it has little competition. The 50 MP cameras have to compete with the A7rIII/D850/Z7/S1r complex - if they don't, they won't sell, since those cameras are competitive in image quality. This means that the sensor has to sell in at least somewhat the same price range, so that Fuji (and to a lesser extent Hasselblad) are looking at a bill of materials that lets them compete, even when they have some other parts (oversize shutter) that are more expensive.
The GFX 100, on the other hand, offers image quality that can only be matched or exceeded in two ways, both much more expensive. One is the Phase One and Hasselblad systems that cost multiples of its price. The second is 8x10" film - the equipment is relatively affordable, but color film is a minimum of $15 per sheet, with processing about the same again. Neither is anywhere near as convenient to use for many types of photography. Sony, knowing this, could be charging Fuji an enormous price for the sensor - and/or Fuji could be charging a much higher margin on the camera because the competition is so limited.
Whether or not either Fuji or Sony is getting an unusually high margin, the GFX 100 is a bargain compared to anything else with that level of image quality. How many people need that level of image quality is another question entirely. My Z7 (if you don't like Nikon, substitute A7rIII, GFX 50, X1D or S1r - it won't change the meaning of the sentence) can drive my 24" Canon Pro-2000 printer to its limits, and has resolution enough for an 8K display, too. Anything above that is for 44" and 60" printers. How many photographers regularly print 40x60" and above for closely viewed display? I'm sure there are some, probably including several people on this forum. For them, the GFX 100 promises to be by far the most affordable access to a new level of image quality.
