I was intrigued by your meta example and I took a look. It took me 3-4 minutes to find the warning, and I was looking for it!
I was expecting a big fat warning on the merge request itself, or maybe on the lines containing the dangerous chars.
In the end, it is a small ? character inserted were the unicode control chars are, and a mouseover tooltip warning about a potential issue.
The warning is good, but why so subtle? Sorry for the criticism. The feature is still a huge positive.