Those dead people in the small row boats weren't on the 'other side' of the Locker. Davy Jones was supposed to ferry these souls to the 'other side', but Jones neglected his duty and now they just wandering / floating around in this sort of netherworld limbo.
TIA DALMA: They should be in de care of Davy Jones. That was the duty him was charged wid, by the goddess, Calypso. To ferry those who die at sea to de other side. And every ten years, him could come ashore…to be with she who love him…truly. But the man has become a monster.
RAGETTI: So he wasn't always…tentacle-y?
TIA DALMA: No. Him was a man, once.
Presumably Jack Sparrow is actually in the 'other side' in the "place of punishment" Tia Dalma spoke of, hence his surroundings are different. If Jones did bring Sparrow to the 'other side', then that would make sense since punishment awaited Sparrow and Jones disliked Sparrow so much.
As for why the ship is down there with him, the films make it clear that the Black Pearl was originally taken to the Locker when it sank, but Sparrow made a deal with Jones, so Jones had brought it back to the surface for Sparrow. Now, in At World's End, Sparrow himself and the ship have both been taken by the Kraken to Davy Jones' Locker (on the 'other side') to a place of desolation and punishment.
From the wiki:
The Kraken dragged the Black Pearl down to Davy Jones' Locker, along with its captain. Both were marooned on a seemingly endless desert.