No one? Bueller? Bueller?
OK, so I may have come up with a solution, I'm just not sure how elegant it is:
I have a seperate install.cfm that handles the scheduled task creation. The file that gets included on application start now moves this install.cfm to the /cfide directory and then does a cfhttp call to it on 127.0.0.1 ... which is bound to the cfusion instance ... thus installing the schedule tasks to the correct instance and making my OCD happy. The file is then deleted once the cfhttp returns correct setup.
Does the job, but as I say, doesnt seem to be the most elegant of ways.