the Hexagonal Part is the size of a M10 Nut, this was to mount the V97V10 Hotend (look at the second picture the right hotend) at first, but is not necessary anymore, the second reason is to make it this deep (20mm) is to put some long hotends into it (Stoffel`s V1 for example).
If not used you can print the hex dummy (and the other inserts) separatly and put it into the extruder as you thought right.
If you use 1,75mm filament you do not need to print it as you can use the brass insert to bridge over the space.
i missed it to explain the hex hole, i added a picture to show it to you.
the two inserts types are the two dimensions of them, one set is with 16,4mm diamenter the other 16,7mm. as the body also has 16,7mm there ma be some people who are not able to put in the 16,7mm version into it printed with their printer.