Really not sure what I am seeing here in terms of comparsion...
Of course looking at an image on the monitor zoomed at 100% doesn't tell how the print of this particular image will look like (grain, sharpness, contrast etc. etc.).
But still two images zoomed at 100% tell something about the difference of the two respective images in terms of comparision.
Or maybe zoom them both at 50%... or if you use OpenGL zoom them both to print size ... either way.
But when you are comparing actual prints you also compare the method of uprezzing, the sharpening technique and you name it.
So the entire printing workflow...
How will the prints look like without resampling, i.e. at native pixel size? For instance if you print the 645D image at 360ppi and the D3X at 300ppi (to achieve a comparable print size).
The Pentax simply resloves more details and the actual image is larger.
You can see that at any (useful) zoom magnification on the monitor.
Therefore it comes to now surprise that the difference is also apparent in a print.
Your 645D processing obviously doesn't match the D3x image by the way. It's darker, less contrasty and the white balance is warmer.
All three aspects are an advantage for the D3x print here... as the 645D looks a bit dull in comparision.
Bottom line... larger prints benefit from captures with higher resolution.
But I was already aware of that before...