In tight spots or heavily trafficked areas, or in areas where boats of all sizes and maybe even people on rafts, kayaks, or SUPs, or even swimming in the water could present safety hazards. Consider trying to navigate out of a popular anchorage in high season. Responsible captains know the importance of avoiding contact and giving a wide berth to these unpredictable vessels, and the flybridge gives them the vantage point to do just that.
Also, navigating a narrow channel can be a challenge from the main-deck helm station. The angle of the lower helm at certain times of day presents glare from the surface of the water, plus the sunlight playing on the windshield, and may make it more difficult to see the channel edges beneath the surface and even aids to navigation in some instances. The higher sightlines of the helm on the flybridge often present a better option and a better view of the situation.