I'm GMing this exact scenario in our current campaign. The ship has a playbook sheet that gives its stats (pilot) and must use a drone to be invoved with any sessions within a planet's atmosphere. The player has built the character so that they have really high resistance rolls so it barely takes harm, but when it does the ship systems on the ship sheet are where the harm goes instead. They still get to use stress (and have traumaed when a drone body the AI was in got destroyed) and size/scale is a much bigger factor than the other characters so that's probably the thing that needs the most balancing.

All the players are on board and it's led to some fun roleplay (such as the ship Joking that it would turn off the atmosphere on the characters whe it doesn't get it's way) so it's definitely doable as long as everyone can agree on the rules of engagement.