One feature handbrake has that shotcut would benefit from is a preview export feature, that would allow you export a 20 seconds to about a minute in length clip to see how that part of the video would look in final export. Handbrake itself does about 10 seconds from preselected parts of the video.
This would be very handy for checking parts of a video with large numbers of filter settings to see if they work correctly. Be very helpful if you could set the timestamp for when the preview starts and ends from.
In the past I have had the odd issue where what happens in the preview window isn’t always what happens in final export. This would be a great feature to test areas of a video you had concerns about. such as when many filter options are used over multiple tracks, or just to preview how a video will look on final export.
I’ve used size and position a lot in the past to resize or video aspect and often do small test exports on the filter to check the resized video looks correct after export. Current this can’t be done as part of a large video and you have to create a project for it or heavily cut a project down, then undo the changes after the export to see the results.