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.