Will that mark the filesystem in use, the same way as a process with that current working directory would?

If there's a kernel thread for kftpd that has that directory as its CSD, then yes. Whether that's true or not depends on how kftpd works -- I haven't looked.

I bet it wouldn't show up with lsof, either...

Probably not. (lsof lists the CSDs of user processes on my PC, but not those of any kernel threads.)

Peter