AFAIK, process groups can not be added or removed programmatically. They need to be defined in fly.toml and redeployed again for changes to take place. Like you mentioned, processes can be added to the machine config but I’m not sure that’s your use case.
Note: Process groups” and “multi-processes” are two different things since the former can be defined in fly.toml as opposed to the latter. There’s no section to configure “multi-processes” in fly.toml
@dangra explains the differences in this post: