For many ports, the ship excursion buys peace of mind. In Kotor, the calculation is different because the Old Town, waterfront and boat-tour docks are almost beside the ship. Cruise line excursions often cost far more for a large bus group, while independent local boat tours keep the group smaller and start from Park Slobode, usually a 2-minute walk from the pier.
The real independent-booking risk is all-aboard time. Reputable Kotor operators ask for your ship name, monitor timing and advertise return-to-ship planning, but your ship is not obligated to wait for a late private excursion. If you book independently, choose an early slot, tell the operator your all-aboard time, and aim to be back near the gangway at least 1 hour before departure.