1) I don't see the point of a button for that, if the menu contains the spawning menu you mention, and when you right click on the directory/file you have a spawning menu as well. Do you really think there is a need for 3 options to do site commands?
2) I can see this being handy in some situations, however IMHO this is a server side thing. The server should be configured to accept these kinds of characters or not. Perhaps in a future version where scripting is implemented this will be possible though.
3) If you just press Control-D FlashFXP will be comparing on file name only (i tested it here and works exactly as you wanted it to behave)
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