I have a question about this mission.

One of the points says At the end of each round the Imperial Player gains 1 Threat for each Homestead tile containing 1 or more fires. Is that on top of the threat already being gained in that mission?

They are separate.

You increase threat by the threat level during the Increase Threat step.

You resolve the mission rule about fires during the End of Round step (after the deploy and reinforce step).

It's also important to note that "tile" refers to the physical tiles you use to create the map and not to individual spaces. Our imperial would have missed that had it not been explained.