Hello, Per
Unfortunately, the present engine is just single-destination.
You've got a couple of choices. The simplest would be to just kick off a separate process to run an external FTP session to the open web server.
Alternatively, if you're handy with Python, you could modify reportengine.FtpGenerator so it can recognize multiple sub-sections in section [FTP], one for each destination. Fork, modify, then I'd be happy to take a look at a pull request.
But, at this point, I just don't have the time myself.
Seems like a reasonable feature.
-tk