A minor issue: on a fresh Geany install (or a clean $HOME folder), this new option is still selectable by default, even if "Show line endings" is deselected. My first reaction when trying to enable this new behavior was to click the option directly, which did nothing (I was expecting it to automatically trigger the new behavior, but you need to select "Show line endings" as well). If I select and deselect "Show line endings", the new feature gets grayed out, which is more intuitive (now it's clear that I need to select the parent option to make this option available, and that this option will only do something when "Show line endings" is enabled). But for some reason, if I've never touched "Show line endings", the default is for "Show only non-default line endings" to be clickable.
(Alternatively, reword it as "Hide default line endings" to make clear that this option _hides_ some line endings rather than _showing_ them, but I think it's preferable and more intuitive to fix the gray-out behavior and leave the wording as is.)