I don't use to many different FTP servers but I have to say I have never had any problems with background transfers. Of course it is possible to configure FTP server for only one connection per user but from my experience it is not very common. I'm happy that you have it on your todo list. I also understand that your free time is limited.
I have commercial license for program similar to Multi Commander and I have to say that maybe MC is currently not as polished as commercial alternative but at the same time it has a lot of useful functions which are not available in other products. I'm not sure if I switch from commercial product to MC in the near future, but I'm really impressed with your work.