To the OP, my perception is that window air conditioners tend to be more "efficient" at cooling the boat than build in systems.
My suspicion is that the window air conditioner has a great advantage of cooler air to work with sitting in the companion way vs. being stuck in a locker, settee, berth ... with limited airflow.
Would the efficiency that is perceived as "cooling effectiveness" be largely influenced by the amount of ventilation the AC has to work with?
In some cases, yes. With a window unit the air is not being forced through ductwork, which, on many boats, is uninsulated. So even if the AC unit is providing the right temperature cold air off the coil, by the time the air gets to the "room" it is supposed to cool, that cold air is warmer, and thus cools less.
A BTU is a BTU. Really. 1 "ton of cooling," a common unit in North American refrigeration and air conditioning applications, is 12,000 Btu/h.
The "supply air temperature" which is the temperature of the air introduced into the space to be cooled is critical to ability to cool, as well as the amount of air.
So a "free flow" wind AC unit could be more efficient than a ducted (uninsulated ducting) unit.
The supply air temperature of 59-60 is also a tad high. Most air conditioning systems, in buildings for example, introduce air at 55 degrees. Sometimes in moderate weather this temperature is raised to conserve energy when full cooling is not required. when it's not as hot outside as it possibly can get on the hottest days of the year.
So, it's not so much where the unit is located, but rather the temperature and amount of air that is applied.