Welcome! Here's some quick answers to your questions . . .
1: No, the cargo cover is not standard on the 2012. If you really want one, do a search here, there is a parts list available to fit one in. Two simple screws and its in there, no drilling or modification necessary.
2: Short answer, no. For Navi, I opted for a TomTom instead of Honda Navi. There are a lot of companies that make rear seat entertainment systems that will go on that back of seats for the kids. Everything from systems that hang on the headrest pillars to systems that are mounted into the seatback. A visit to a local car stereo shop should find some options. As to the b/u cam, my 2012 EX-L came with one in the rear-view mirror, yours should have too . . . maybe it's turned off? (button on mirror).
3. The body side moldings are simple. The Honda kit includes templates and alcohol wipes. They come color matched as well. You just use masking tape to put the template on, wipe down the area, then peel and stick the moldings. Door edge guards are a little trickier, they are in essence nothing more than thick mylar tape.
4: Vinyl or Leather surfaces? For leather, I like Lexol. http://www.lexol.com/