Nearly all SD video 4:3 or 16:9 has non-rectangular pixels. Shotcut has the video mode “DVD Widescreen PAL” that matches his timeline properties.
It looks like there is something going on to cause an aspect ratio issue when 32 pixels are remove from the top. It is not as simple as 16 are taken from the top and 16 from the bottom even though it may look that way. Because it appears that black columns are added to the left and right. This is probably a defect in the crop filter and how its output feeds into the automatic scaling and padding. You might be able to work around this by cropping on some other edges.
However, from the Media Info, I can see 2 other reasons you might want to convert this as Namna suggests. Shotcut does not have a field-aware scaler, so if you change the vertical resolution as you are doing, it invokes a deinterlacer. Secondly, this MPEG-2 Video is encoded with an open GOP, which is not reliable for editing if you plan to do that.