edit: maybe i should tell a bit about the files that get overwritten... when i take a video with my camera (panasonic, also in the past) the camera adds an jpg with the same name as the video containing important meta data about the video, like when it was taken and with which camera, something i always found very elegant. the image belongs to the video. by doing a cleaning of the coverart folder or when i take a new screenshot, these images are overwritten.
I'm not sure exactly how the cleaning function works, but I assume its purpose is to clean-up the cover art folders so they would include only the images not maintained beside the media under the new system. If that had been done at the time of the change, and covers were previously saved in the separate folder, then there would be nothing to overwrite. I'm not sure if the function has any purpose beyond that one-time use. If it does, however, then there would be no images in the video folder that could overwrite covers saved beside the media.
Why would you
Use Screen Grab for Thumbnail when you know that's going to overwrite an existing cover you want to keep? There is a
Screen Grab to File... command for saving the image with a different file name. If you do this often, it would probably be easier to routinely copy the camera images to a different filename (e.g., {video filename} [camera data].jpg) so they're preserved.