> "if you are using the C locale you or the OS are broken anyway, so we'll just pass the bytes through"

Exactly. Even if you use Unicode, the Python 3 str type, you store text as raw bytes (in a custom format, as surrogate characters).

> I'm not entirely convinced this won't cause issues, but I suppose it might not cause any more issues that having things break due to the C locale does.

The most obvious issue is the come back of mojibake. Since you manipulate raw bytes, it's easy to concatenate two bytes strings encoded to two different encodings.
https://unicodebook.readthedocs.org/definitions.html#mojibake

The problem is that the question is not how bad it is use to manipulate text as bytes. The problem is that a working application written for Python 2 starts to randomly fail (on non-ASCII characters) on Python 3 when the LC_CTYPE locale is the POSIX locale ("C"). The first question is: should I keep Python 2 or write my application in a language which doesn't force me to understand Unicode?