A lesser magnification is an advantage, but an old, pre-BSI sensor is a disadvantage. From what I've been able to see from looking closely at prints from the Fuji 50 MP cameras and making prints from my own Z7 files, the two just about cancel each other out.
This is not to say that the 50 MP cameras are bad (at all)... Just about the same as the very highest resolution 24x36mm pixel monsters is darned good. Both are far more than good enough for most applications. It's just that they don't seem to have a unique advantage over those few 24x36mm cameras.
If it is a loss leader chip sold for the same price or less than a top 24x36mm chip, then it makes a lot of sense... Fuji can offer a camera that is somewhat price competitive with the 24x36mm pixel monsters and has an upgrade path to the GFX 100. They have a few extra build costs over Sony or Nikon, even if the chip's around the same cost. They aren't making as many of them, nor are they sharing a lot of parts with a cheaper, higher-volume camera (a few shared bits, and a lot of firmware, with the X-series, but not like the Z7 and Z6 or the A7rIII and A7III).
They're also running at a higher voltage, using a custom three-cell battery that's not really related to anything. There are several basic sizes of the usual two-cell battery, but a Nikon EN-EL 15b is a very close relative of a Canon LP-E6 or a Sony NP-FZ100, just as the smaller Fuji W126 is a relative of a Sony FW50 and several others. The Fuji MF battery (T125) is actually the same voltage as the D5 and 1Dx II batteries, in a much smaller package with a much lower capacity (mAh).
None of these things make a huge difference in cost compared to a Z7/A7rIII - that's why the GFX 50R can sell for as little as it does. Hasselblad is trying for a slightly different market, especially with the expensive lenses. Of course, the problem (for both companies) is that, once Sony runs out of however many old 50 MP sensors they have stockpiled, they either won't be willing to make more, or will charge much more for them. I wonder if I'm right that a big order (quite possibly from some three-letter Federal agency whose employees favor trenchcoats) might have gotten cancelled? If so, how many sensors is Sony selling as loss leaders?