Many port stops do not have enough private vendors to allow most of the pax a private tour
How many guides would be needed for 1000 pax to do small group tours ??
Ships tours fill a larger quantity of people for the same destination & often employ those that would otherwise give small private tours
I have booked small group tour up to 12 pax in many places but finding a guide in some locations can be tricky
If you can find local guides great if not a ships tour can work for some
There is no right or wrong way
YMMV