I do not have that limitation, especially for a portlet since I only have to run it in our Dev environment. Once I'm done building it in DEV, I XOG it into Test and Prod. However, I have had the same issues when I make changes to a view which would require me to run the job in all three environments. That being said, couldn't you just schedule the job to run at least once a day and therefore you know your configurations will be done on the scheduled time.
Either way, any of the suggested solutions, XOG out and then back in or run a job, should not have to be done. PPM should automatically reflect the changes you make as soon at you hit SAVE.