I have a similar problem, but I have the option ticked off. Not sure why a newline is appended.
Either way I think this should not be the default that the editor is making changes to the content. The original content was x; geany appends a "\n" there means that geany modifies the original content. I don't think this should be done by default.
Note that editors such as vim or nano don't do this either. I don't think it should be the default. Right now this annoys me immensely, even if I am hitting this due to some bug (e. g. I have the check-box unchecked but a newline is still appended, so I can not really control geany's behaviour right now.)
It's ok as an option of course.