For reducing external dependencies, it would be nice to somehow know every call made to a package, generating the call tree to replace. That becomes the API of the internal, replacement package.
Consuming a package also means following its development alongside one's own. Multiplied by each dependency, it's a commitment to a particular constellation of dependencies. Migration guides and codemods help, but ultimately maintenance requires active participation.
That takes time--often more than what's available.
That might get you part of the way there.
Frankly, I don't see how the node ecosystem can ever be secure. It's random-libraries all the way down. With half of them being useless frippery.
Imho, WASM compiled from languages that have strong standard libraries are the way forward for security. And, maybe node will get fixed in 5-10 years.
A good example of a language going "this shouldn't be a library."- Net used to only have a third party json parser (newtonsoft) but microsoft created a first party json parser and deprecated newtonsoft from their examples and templates
A partial or semi-automated, tool-assisted approach might be possible, if there were a way to restart Node.js between decisions. Each decision point writes an entry "event" that records the filename, function, caller, line number, etc. Then `debugger' is inserted before the next line, and so on.