But I still don't see this as a problem. Allowing arbitrary encodings, arbitrary mix in an single text stream of right-to-left and left-to-right rendering, homonyms and visually identical rendering of different byte sequences are all a problem, and in particular when any of these are being used across a web or OS interface, where recognizing the intent is quite important.
The problem is not Unicode rendering. The problem is improperly mingling information of a different nature. File extensions are not a good way to tell you if a file will be executed (Unix got that right from the start). Then executing a file involuntary shouldn’t lead to significant risks for your data and your system. That’s the actual problem which needs to be solved. Mangling text rendering is not the solution.