It depends on the shape of it. If it is square-ish it will probably work. We are having problems generating all of the outputs for jobs that stitch together and the resulting GeoTiff is over 65k pixels in any direction. We convert it to GeoTiff but then a couple of our other conversions don't work. If it is square and has sufficient overlap it should probably work. We have done lots of jobs over 20 sqkm but they had pretty big GSDs. Our current upload limit is 1500 images to keep people from posting jobs that are too big.
Submitting them by quadrant would be best. Long thin jobs don't turn out as well.