No, unchecking the filters have no effect on rotation, so why not merge size and rotate as a filter, so that the focus is consistent, and rotate can control the size to rotate so that it is not cropped
Both Size and Position and Rotate and Scale use the same underlying filter in the engine. They are likely conflicting and can be merged into one filter. However, the merging probably requires that rotation support be added to the on-video rectangle control since that is what people will expect. And then to figure out how the scale slider would interact with the rectangle size. I will likely revisit this area at some point, but it is not an urgent bug for me to address.