Panic just posted an update on the situation via Twitter.
In the previous version of Transmit,Apple was displeased with the apps capability to send files to iCloud Drive.
Because the share sheet with the Send to iCloud function is completely controlled by iOS, Panic had to remove the entire page. That decision also removed other features like send to Dropbox, Box, and other services.
This is the second major flip-flop from Apple in a little more than a month. In October, Apple told PCalc developer James Thomson that he must remove the apps iOS 8 Notification Center calculator widget.
After an outcry, Apple changed course and will allow PCalcs widget, and other calculator widgets, to remain.
Apple has also asked developers of other apps like Neato and Drafts 4 to significantly modify their widgets or risk being removed from the App Store.