Shotcut, via FFmpeg, expects sources to have straight (unpremultiplied) alpha values. Overlays do not work correctly if the input has premultiplied values instead. The suggestion is to add an option to the Properties panel that allows the user to select between Straight and Premultiplied Alpha when the input contains an alpha channel. The selection can be passed through to the alpha option of the FFmpeg overlay filter.
We do not use FFmpeg overlay, and that will not be added. We use frei0r cairoblend and Movit overlay neither of which accept an only pre-multiplied alpha.