In NPM's run-scripts, user could set custom NPM env (entry with npm_config prefix) via CLI parameter:

npm run <name> --my_custom 

which generate npm_config_my_custom=true for the executed script.

Verifying it easily, I use npm run env with custom parameter:

npm run env --report | grep "my_custom" 

This feature is not present with yarn yet. I am wondering if the core team would consider implementing this feature at all.