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Howard-
The external junction box sits under the bottom bracket where you would normally attach a cable guide.
It all depends how they want to route the cables, but they might want to use that if the cables aren't long enough to reach the rear derailleur from the battery, it may not be necessary though, as you say the external battery mount contains a junction box anyway.
danb
Only if the want to run the cables externally and join them externally :)