Thanks for your feedback.
I've got a box that's pretty heavily IO-bound and has a BTRFS filesystem, this causes the "host is not communicating for more than 15 seconds" dialog to be present between every file that I upload, and because it's a modal dialog WinSCP sits there blocking access to my desktop. I also can't change tabs while it blocks me.
Modal dialogs are pretty inconvenient and old-fashioned and really ought to be used only as a last resort. Maybe a notification bar would be a better idea in this scenario.