Thanks you for your interest
1) I will be honest, I don't know what the encoding is for in the rcon options. It's used in the node.js package I use, not sure why.
Link to the docs.
2)
Here is the doc to the FTP uploader:
ftp deploy
a)
It will upload everything in the Desktop yes, except for scripting, .vscode, etc You can change that in the include settings
b)Details in the docs above
c)RCON passwords/hosts and SFTP passwords/hosts are usually not the same, so it's useful to be able to separate the two. This can be redundant if you use the same credentials.
I have started writing some proper documentation, it is available
here.