The campaign doesn't seem to have the ability to progress if you managed to save the transport from the enemies in M1. I looked through the scripts for M1 and I couldn't find anything that would act as a safety for this. I also didn't notice the console messages during my first go at this campaign, which is why I saved the transport. It was also a little misleading since the transport could still hover and was at 100% health when it was supposed to be incapacitated.
I'm not sure if there's any way to do this with Warzone's engine as it is, but if you started the transport at a very low health and dealt damage to it through the script to kill it once the Nexus units start attacking it (not immediately), you could prevent the player from breaking this part. Or you could give Nexus air units to destroy it, but this could instill fear in the player that they will have to deal with Nexus air units and build AA defenses when they aren't needed.
Less important, but still something to consider. The dialogue is a little vague. IIRC, during the game's campaign, the player was usually warned of an attack or nearby base, but was also given a definitive order of what to do. For example, instead of saying:
Commander, we're detecting an enemy Recon Force heading our way to finish us off. I suggest we head north to evade them. ETA: 1 minute 50 seconds.
You could say:
Commander, we're detecting a Nexus Recon Force heading our way to finish us off. Proceed to the north to survive the attack. ETA: 1 minute 50 seconds.
Changing enemy to Nexus and evade to survive would also help push the player in the direction they're supposed to go. The player might think it's just a scavenger recon force attacking since that's who they'll see surrounding them. And if someone sees a suggestion
to evade a recon force, they might decide to stay and fight, especially if they think it will be a bunch of scavengers.