KOReader comes with SSH, so you can just SSH into it.
To be fair, it is now possible to load your favorite fonts onto baseline Kindle.
Hmmm not really my experience, unless it's a new thing. I am still able to access it via finder. Although I need to exit KoReader first and go back to the stock UI.
I can recommend using a Filebrowser plugin for KOReader, that way you can access the file system over a web interface and upload that way. No cables needed or anything, quite convenient.
I use OpenMTP rather than Amazon’s software, and that works fine for me.