Well, the thing is, if I add a standard folder it doesn't ask me that confirmation. It only asks when I add an encrypted folder. It's more about UI consistency. Actually, the thing that bothers me the most about that warning is the word "destination". I'm choosing a *source* not a destination. This leads to questions that @PaulU correctly deducted.
The next thing that I find strange is that if I already have a standard folder (that is currently syncing on multiple machines), then it should be possible to add an encrypted target to that mesh. Currently I can only see the RO and RW keys. It would be really great if you could add a feature that "converts" a standard RW/RO keyset into a RW/RO/E keyset.