While I was sme coding I had to take a look at the original FS2 missions to see what red-alert-carry-status had been used for. Rather than simply open up SM3-09 and check I simply grepped all the missions and found something a little surprising. Although
Clash of the Titans II is the only mission that ends in a red alert, it's not the only mission with ships set as red alert. Even more interestingly, even though red-alert-carry only works with fighters it has been set for several other ships.
Now some of this is probably just simple mistakes but some of it is obviously by design and gives us a glimpse at the early mission designs and script of the game.
1)
The Place of Chariots and
The Romans Blunder appear to have been designed as a linked pair of missions. The Freighters in the first mission appear in the second one and have been set to carry cargo containing the same things. Both freighters and cargo have been set to red alert.
2) Rather bizarrely the Sathanas is set to red-alert in
High Noon. Not entirely sure what that means. It could be a simple mistake or it could be an indication that the Sathanas was meant to accumulate damage from a mission proceeding it (There is a systematic error in the :V: missions where they set red-alert-carry on both the mission proceeding the red alert and the red alert itself).
3) The Azrael that carries off Bosch in
Return to Babel is also set to red-alert.
4) Most interestingly of all, Alpha wing in
Their Finest Hour is set up to red-alert. I tend to feel that this is good proof that originally the last three missions were meant to run back to back. This probably proved too difficult so the first mission was turned into a stand alone.
Now if that's what I could glean simply from a single ship flag, I wonder what else becomes more obvious if you take a good look at the missions themselves.