Pentax 645D has a
40.0MP Medium format (44 x 33 mm ) sized CCD sensor and features Prime II processor. On the other hand, Fujifilm GFX 50S has a
51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features X Processor Pro processor.
Fujifilm GFX 50S's sensor provides 11MP more than Pentax 645D's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Pentax 645D's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the 645D and GFX 50S sensor size comparison.
Pentax 645D and Fujifilm GFX 50S have the same sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Pentax 645D has 29% larger pixel area compared to Fujifilm GFX 50S, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.