"Unix programs" I haven't ran into throwing a fit per se. That's why I didn't write that.
What I ran into issues with was contemporary software that's shipped to Linux, such as Neo4j, which expects its license files to have no newline at the end of the file, and will actively refuse to start otherwise.
I have a feeling I'll now experience the "well that's that software's problem then" part of this debate. Just like how software not being able to handle CRLF / CR-only / LF-only, is always the problem - instead of text files being a joke, and platforms assuming things about them being the problem.
What Unix program "throws a fit" when encountering a perfectly normal newline in the last line in a file?