I have no specific knowledge, so take this with a grain of salt.

The article comments "Yuck. It works, but it certainly wouldn’t pass code review. Here’s what we really want:"

This shows that what's needed isn't simply a transpiler, which only needs to be technically correct according to the language semantics, but rather a transpiler which generates maintainable source code.

The "--loose" option gives another example of how maintainability might be important enough as to prefer a possibly incorrect transformation.

CoffeeScript and JS are semantically quite similar languages. COBOL is nowhere near as close to C/C++/Rust/etc. This makes it much harder to generate maintainable transpiled code.

Finally, the author's company developed "tools to help biologists coordinate experiments, analyze and work with DNA". A bug in this sort of environment has less severe consequences than (say) in the banking industry, where there are laws and regulations to follow, and where people's money might be on the line.

That is, banking has a lower risk tolerance for the sorts of errors that might sprout up in large-scale automated source code conversion.