There difference you found there is the one between a troop transport and a dropship.
Troop transports are regularly civilian, due to their high size, and essentially you can take your average freighter and convert it to a Troop transport.
They will load and unload very slowly, so I recommend putting cargo Handling on them.
As for Combat zones, a CiWS and extra armor will protect it well, 3 is actually very good for a non-combat ship.
However, if you want to board ships or Assault Planets, you might need a dropship, which is a military design because of the much smaller drop modules.
This is the point where Cargohandling will become crucial, and given the size of your smeg, extra handling modules won't hurt it too much.