EDIT: Sorry, I understand you're talking about package.json. Would be fun to try to get the Node & package mgmt teams aligned to add support for comments in the package.json. Bun tried and failed to do this (requires ecosystem coordination).

Nub could absolutely support a config file and use it to set NODE_OPTIONS or flags in the node child process. There's no reason to throw out the baby with the bathwater due to DX concerns like this. That's a key part of the concept Nub is trying to prove. (To be clear I'm quite content to conform to Node's no-config-file policy at the moment.)