Sorry, sorry, sorry. I forgot about the change in coordinate systems after proxy support was added to Shotcut.
Before proxy support, the pixel values in Crop: Source referred to literal pixels. After proxy support, the “pixel” values became relative to the project timeline resolution rather than the source video resolution. This is what allows a crop value to remove the proper amount of source video when the size changes from full-resolution original media to quarter-resolution proxy media. Otherwise, literal pixel values defined for original media would remove too many pixels from the smaller proxy media.
So the new math works like this…
As we mentioned earlier, a 1080x1920 source video would have to be shrunk to 608x1080 to fit within the project resolution of 1920x1080. (Technically, I think Shotcut might truncate decimals to 607 instead of rounding 607.5 up to 608.) Even though the crop isn’t happening on the shrunken version, the crop values are still based on this shrunken version. This provides a common base for determining a percentage amount to crop when switching between full and proxy resolution.
So, if there is a 608x1080 video on the timeline (after fit-to-timeline resizing), how much crop do we need to do to turn it into a 16:9 aspect ratio?
608/h = 16/9
h = 342
So, lifting a 608x342 crop out of the 608x1080 video would give us a 16:9 aspect ratio.
Then, we ask how many pixels we have to crop from 608x1080 to get down to 608x342, and the answer is 1080 - 342 = 738 pixels of height to crop (in timeline resolution units).
When the “Crop: Source” filter actually processes the video file, it will calculate 738 “timeline pixels to crop” divided by 1080 “timeline pixels of height” equals 68.333% of the height to be removed. If the original source video is 1080x1920, then cutting 68.333% of its height turns it into 1080x608, which is a 16:9 aspect ratio that upscales nicely to 1920x1080. Likewise, if the source video is a 304x540 proxy of the original, then cutting 68.333% of its height turns it into 304x171, which is also 16:9 aspect ratio, and enables preview playback to work in proxy mode.
It’s a little convoluted due to proxy support, and sometimes it’s just as easy to eyeball it until it looks good. 
But there is a good reason for the complexity.
Here’s another example of the math when changing aspect ratios, if interested: