Your #1 and #3 are unexpected, non-standard behaviour. Middle-click in X11 is expected to paste the current selection, not something unpredictable that may have selected at some point in the past.

If you want to select something without clobbering your "copied text", e.g. in order to select some text and paste over it, then you should not be using the primary selection. Most programs -- including Padre, I assume -- support the standard Ctrl+C/Ctrl+V setup using the clipboard for this kind of operation.

#2 and #4 are both acceptable behaviours. Emacs provides a configuration option to choose between them.

I personally favour #4, because I find it easier to get the text cursor in the right place than the mouse pointer. It can be very difficult to middle-click exactly where you want text to be pasted, particularly with inaccurate pointing devices such as laptop touchpads.