1) MoonXX is the ID of the media directors (Relates to the Pluto origins of this stuff) They seem to be detected even though they should not be. This is a known bug (fwiw).
2) The detection scripts come from having some unrecognized serial device somewhere.
3) The DVD changer should work but its a little buggy. if you can check its logs when its running you may see lots of errors. A second changer should be able to make its content available to a second system.
4) No need for Gigabit Ethernet for the HDHomeRun. It can manage fine with 100M E.
5) Shared folders on the external network are not normally available, there are a host of reasons to keep the two seperate. But you can move all of your network stuff to the inside network, leaving only the cable modem/DSL modem on the outside.
6) You can change add and delete MD's (except the core) at any time, but it will take a while for the system to do the work.
7) Don't know about DVD Audio. Am working on Bluray but no promises.
You can integrate and control the DirecTV stuff but not internal, LMCE becomes a big remote for it. However someone found a way to get a Sat device into Myth (I'm not sure which) so there may be a better integration in the future.
9) I would use the changer unless you expect to watch the movies over and over a lot.
10) I set the system to Flac for best audio quality.