So I just found this: http://alivemod.com/forum/1226-auto-generated-task-editing/0#p3954
This thread was also attempting to limit the types of C2ISTAR tasks that generate and I can also verify that I have the exact same issue with the script in this thread. There's a variant of it in the link above too.
What I can't discern is if "clear the town" is the only one immune to the script (when "CivAssault" is removed), or if the script only works on the first task; meaning the script has no way of getting reinitialize once the first task is finished. If the former, there's at least hope that if we can find a way to get the script to disable that task, then everything should be good. If the latter, and the script is just not designed to work in MP, then maybe someone with some scripting knowledge can find a way to get the script to reinitialize after the first task?
What I can say for certain is that inevitably, "clear the town" is going to eventually surface and then the entire auto-tasking process breaks. The "clear the town" task either needs to be deleted at that point from the commander tablet, or forced "succeeded" from the tablet. When you do that, the only way to get auto-tasking to work again is to disable auto-tasking (which for some reason forces a new task), and then reenabling it (which causes all of the blacklisted tasks via the script to start generating again).
This is a strange issue. For any dev reading, the thread above is probably the most accurate description of what is happening. I can't really make heads or tails of it but what I do know is several of the tasks are broken, with "clear the town" causing the most havoc.
I just can't tell if the script is only working once of if "clear the town" is somehow immune to be blacklisted via the script.