Quick question, can I set a pulumi config from within the program or is it CLI only?

You can provide any values you want pulled from wherever you want inside the program. They won't strictly be "pulumi config", but you can use them to parameterize your deployment. What's the exact scenario you have in mind?

I’m writing a state machine and would like to change some configs based on certain scenarios. I guess I could also just read in the output of the same stack and change the output after every run?