You are correct that Cyberduck is not dual-pane, but I’m only excited by a dual-pane scenario when I’m trying to compare a local file set with a set on the server. As for having multiple servers open, with Cyberduck, I approach it in two ways, depending on the servers I’m accessing.
In the first case, you can open as many connections, including to different directories on the same server, or just different servers. Cyberduck will remember these windows and their positions between restarts, and so it’s just a question of training your brain s to what window connects to what instance.
Second, Cyberduck supports macOS Tabbed windows, so if you only want one window with all your connection instances, you can cycle through tabs as you like.
Sadly, they dropped AppleScript support many years ago, but you can still whip a little Keyboard Maestro to help manage/manipulate windows/connections, etc…
I only offer up CyberDuck because it’s so much more affordable, as it’s free or donationware; and it’s “good enough” for most people.
Transmit iOS was (is; still works on iOS 12) absolutely fantastic; it worked well with Shortcuts (née Workflow), and played well with Dropbox, iCloud, et al; and it synchronized nicely across platforms/devices.
I didn’t care as much for YummyFTP as I did YummyFTP Watch, and also being able to set up YummyFTP shortcuts for drag and drop for less-skilled clients/employees. Yes, the developer (Jason?) was super helpful and responsive. Sad he threw in the towel.
If you’re doing a lot of drag and drop, window to window, from your local device to your servers, maybe you should instead be looking at scripting and terminal? There’s also tons of ready-made scripts out there, easily customizable.
There’s nothing like a right-click to a menu command, or a Service (free; builtin to macOS) or Macro in something like Keyboard Maestro, FastScripts (free with limits), etc., etc., which can be set to a keystroke or menubar itms or pallet items, to quickly select a Finder item(s) or open document (such as TextEdit, Preview, whatever) in your active application and send it to your desired server path. It’s pretty easy to get directories and file paths with prompts to direct as neededand skip a GUI FTP client altogether.