I don't think the old version did that, never tried it, but this one does. In panucci.conf you can set if you always want the same start folder, it's the "default_folder" option. If you want panucci to automatically remember the last chosen folder you have to comment that option out.
You can add as many files as you want. I have never used 0.3.x but I can't see that it's more work to clear the playlist now. Otherwise there have to pop up a window every time you add something to the playlist asking if you want to delete the current playlist or just append the files. Adding more buttons is not an option either on n900 as the display is too small. There was however a suggestion to add a pop up confirmation window when clearing playlist but I haven't done that yet. That will introduce one more step also.