What I've also experienced is a whole ecosystem has been built up in other departments in the organization (but outside of development) around the crazy CSV file formats, eg: Marketing uses it to trigger campaigns; Accounting uses it to reconcile live accounts; Support uses it to find accounts.

So anything you do to make this better means you now have to deal with this ecosystem. At best, you're solving some pain point these groups have and they're happy about it, but in most cases you're probably forcing unexpected, extra work on them to "fix" something they perceive as not broken. At worst, you don't discover they're even doing this until after you've changed it, and now you just broke a production system you didn't even know existed.

In some cases, the hack another department put in place will also have their own ecoystem built on top -- it's turtles all the way down.

How bad this situation is directly corresponds to how your organization has grown and how siloed different departments are. And keep in mind we're talking about a fictional but easy-to-understand "emails in a CSV file" problem -- most of the real-world problems are significantly more complicated.