I personally have never done this, but I came close once. I do know that some players have reported being able to successfully defend the Plato during Mission 5, which in effect breaks the mission. I haven't played the latest Port version, so I don't know if anything has been done with this or not. I recall some debate about how to solve this dilemma though. One was to simply have the Plato a self-destruct order if all the Shivans are destroyed. The second, would be to introduce a new threat into the mission which cannot be defended against, such as having a number of Basilisks jump in at medium range and with a good-secondary-time event and launch a volley of Phoenix against it, which cannot be intercepted. The third, would be to allow the Plato to escape in that event, but there is of course the issue of the event not corresponding to recorded messages. There is an option of recording new messages, but the voice wouldn't jive existing ones. In any case, if the mission were altered to allow the Plato escape if it is successfully defended, and giving a bonus objective, led to another thought of mine, that could give the player an advantage in a later mission.
Since the Plato was carrying the Avenger prototypes, it could be argued that if the Plato had survived, it might have expedited the Avenger's development, which could mean getting the Avenger one mission early. My thought was, if the player succeeds in the afore-mentioned bonus objective, allow only one avenger cannon for "Pandora's Box". I'm sure many of us wouldn't have minded having even one cannon for that mission. On top of that, add a bonus objective if the player can successfully destroy all Shivan fighters... and of course add a withdrawal order for the Taranis if its in danger of getting disabled/destroyed.
I doubt that the team would support such changes to the originals, but it's a cool thought.