The 'remote on', 'amp on', whatever... that comes from the MkII cradle behaves like the one on the MkI, ie on whenever the display is on.

But the tuner module for the MkII has its own 'remote on' which, AFAIK, is on only when you have the tuner selected. Can for instance be used to feed the antenna amplifier (via adapter) in newer VW, Audi, Seat etc.
To power a motorized antenna you'll probably need a relay, unless one is built into the antenna and it has a separate, constant +12V feed too.

If you go to http://www.tempsch.org and click on the empeg MkII link in Contents, you'll find a pic of the tuner module remote line connected to a VW antenna adapter.

/Michael