I have a node-red flow that pulls in env variables from a process.env node but I can't seem to find where exactly it is setting those values in my project.
I presume you mean
node-red-contrib-process-env. I have not used that but looking at the readme I assume it is the system process environment that it is accessing. System environment variables can be set in many ways. Which variables in particular are you referring to?
This might help: Using environmental variables (system or user defined)