This approach might work.
Define a utility table with the needed fields to document the job that needs to be run.
When an action from an IWP user triggers the need for your "non IWP" script to run, have your script create a new record in this table logging any needed specifics.
Set up a server schedule to run a script once a day (or any other practical interval) that checks this table for new records, performs the specified tasks and then set's a value in a field in this table to log the fact that the task(s) have been completed. If there are script steps that are also incompatible from the server side, set up a FileMaker "robot client" to run the script at a scheduled time.