The ssh to the media directors is not a surprise. See http://wiki.linuxmce.org/index.php/Logging_In#Media_Director
- ssh into the core, then do:
sudo ssh moon##
where "##" is the device number of the media director.
Your boundary issues are not a surprise to me either. From what I've seen, the AVWizard settings only affects the On-Screen Orbiter. I've not been motivated enough to set boundaries for the other applications - I'm only losing about 4 pixels on each side.
I believe the myth update is run by "mythtvuser", which uses /home/mythtv/ as a home directory. I'm not sure though. It happens automatically - look in mythtv configuration for the name of the LinuxMCE script in change of such things.