A few years ago, it was requested in the NppFTP repository’s issue tracker, but the maintainer didn’t have time (at least then) to take on the effort of adding all the DarkMode hooks.

I’ve pinged the issue, and updated with the current state (because in the original issue, even the Profiles and Progress panel was still white, not just the Output and dialog boxes) – but the maintainer asked for help 3 years ago, and no one volunteered, so it’s not likely to happen any time soon, unless someone new volunteers. (@chcg is highly involved in a variety of plugins, plus contributes to the main app, so doesn’t often find time for requests like this; hence the 2021 request for help, which was unfortunately ignored.)