Earlier this week, Panic was forced to remove Transmit's ability to send files to iCloud Drive following a request by Apple. Fortunately, Apple has reversed their decision (as it happened for the PCalc widget) and a new version of Transmit has been released on the App Store.
As I argued last night on Connected, there could be an issue within Apple that leads to confusion with apps that can be promoted and rejected at the same time. We don't, however, know the extent of this probable issue, and I don't think speculating about internal conflicts is worth much (as with most things Apple, speculation isn't useful).
We can (and should continue to) point out unfair and unreasonable rejections, especially for apps that aren't made by popular companies such as Panic. Hopefully this latest string of questionable rejections and reversals will allow Apple to improve their internal App Review processes and make sure these cases become less frequent in the future.