Hard no.

Initial code would still be developed by SME, who:

- Don't understand most programming abstractions

- Don't see the advantage of a clean codebase

- Would rather go back to their code spaghetti mess, than help figure out why some corner cases behave differently in a fresh codebase

- Would still submit changes to their code spaghetti mess and expect you to apply them to the cleaned codebase

I did what the author suggested (not in genomics, but in a different research-heavy scientific field) for a while and would not recommend it to anyone.

And that's not even taking compensation and work conditions into account.