That really is the elephant in the room where SDR is concerned (along with front-end). More realistically you could change protocol/encoding after launch.
Not necessarily. I've never heard of anyone doing it for space (maybe SpaceX?) but you could have an SDR driving a massive MIMO/beamforming array. The SDR can then dynamically "change the antenna" (change the radiation pattern) with a fixed front-end.
One use case I have imagined is being able to have a single radio module that can be used with a variety of front ends, but honestly I am not sure how big a market that is. Certainly I don't see SDR adding much value to high volume applications.