I suspect the problem is less that it discourages than that it does not encourage.

Which gets back to the posted article. REPL-driven development permitted him to feel confident without doing his usual process, it didn't discourage decoupling, but it didn't encourage decoupling either. TDD, to be done well, almost requires decoupling your code to make it more testable.

The same may (I'm not sure I agree, but I've never used Jupyter notebooks) be true of using notebook-styled development approaches and modularity. If the workflow permits relatively easy (and mostly safe) development without encouraging modularity, then it's incumbent on the developer to bring that discipline into the workflow.

And unfortunately, most of the new crop of programmers don't have that discipline. I tell them to write tests and they eyeroll when they think I'm not looking.