Yes, physics indicates that a 50 MP small medium format sensor will have higher image quality (all else being equal) than a similar pixel count (or the hypothetical 65 mp) 24x36mm sensor. I'm assuming that the question is low-ISO image quality with a great lens in a big print (why else consider medium format)? In the present case, all else is not equal. Image quality on the same size/pixel count sensor generally increases over time if you're looking at the same technology tree (in this case, all relevant sensors are variants on Sony CMOS).
The 50 MP medium format sensor is the oldest Sony sensor in any camera manufactured today (it's a 2014 sensor), while the 42-45 MP generation 24x36mm sensors are relatively recent, with several technological improvements since 2014 (BSI, copper wiring). Any Sony ~65 MP 24x36mm sensor would be the very latest generation, with further improvements.
The question becomes: will more favorable physics overcome several years of technology? In the case of the 50MP sensor versus the Sony/Nikon 45MP, my answer from looking at big prints very closely was "generally either tied or a very, very slight advantage to the big sensor, but by so little you'd need a magnifying glass to tell, and certainly not by enough to make the weight difference for camera and lenses worth it". A 65MP sensor with another couple of years of technology advances would probably beat the venerable 50MP sensor.
Of course, none of this holds for the 100 MP small medium format sensor. THAT is technologically recent, larger, and holds a substantial pixel count advantage (plus 16-bit readout). That sensor should beat any 24x36mm sensor for the next several years.