Hi guys, I didn't read everything below in detail, but I just wanted to add that the Pymakr package for Atom has an option for not rebooting after upload :) No need to switch to FTP if the reboot part is the issue.
Actually, VSCode is supposed to have the same option, but when testing it just now it shows a bug (it doesn't show any output in the terminal after upload). I'm going to fix that now and add it in the next release. After that, you can add "reboot_after_upload" key to the global or project config file ("reboot_after_upload": false) and it will not reboot the board after uploading or downloading.
Good to hear you sorted that out @theshade! If I have time I might fix Pymakr to look in that folder on a raspi, although I think there are not many people running this setup. (ps Pymakr is open source, so if you want to do that yourself with a pull request, feel free)