A separate battery works fine, as long as the connection wiring is long enough to position it far enough forward to be out of the way.
I too went with the Torqeedo, but purchased the Ultralight 1103 AC unit to minimize the hardware potentially interfering with the rudder, main sheet, traveler arrangement I have. A bit heavier (about 33 lbs including battery), but It works like a charm and has excellent range at partial throttle.
The bracket stays fixed, but the propulsion unit just drops in and out. More info here
https://www.hobie.com/forums/viewtopic.php?f=9&t=69418 where there is a link to photos showing the position of my battery.