I believe that for the moment the answer to all of these is mostly no, but they are all good things I will add to the list of feature requests.
1 - There is a new option to move media files embedded in the wiki into the /files folder inside the wiki folder, but it doesn't have any affect on other embedded files.
2 - No, I will add this. It is a good idea.
3 - I don't think that there is currently a way to do this. It should be simple to add one to Bob, I am not certain about other ways to use tiddlywiki.