For a bronze age culture, to have all the structures and buildings made of apparent metallic structures leaves questions of mettalurgy and technology.
The Ferengi shuttle is supposed to be the same one brought with the two Ferengi in the Next Generation episode. In that episode the cockpit was dark and cramped,
however here it is light and spacious. Even the control console is larger. The Ferengi could not have done the modification required as they were supposed to be stuck on a primitive planet since they arrived.
One of the security guards (the unnamed Chinese/Japanese one, not Murphy) summoned to the transporter room by Chakotay to remove the Ferengi was not wearing a comm badge.