Well, the relation you make is true in one sense, in that in Naval applications the engines could be made to run cooler since you have an incredible heat sink available in the ocean water itself.
It is, however, largely irrelevant to compare Naval applications to railroad applications except in the simple sense that you can truly say that the engines were completely successful in their intended roles in shipboard use. (The submarine I served on for over four years had, as a standby power source, a six-cylinder 38D8-1/8 engine with which I was intimately familiar. Of course, the primary source of power was the reactor.)
Robert Aldag (a former F-M employee) has written extensively about the development of the engine and modifications thereto as regards locomotive application, and the relation you make is a partial quote of material he originally presented in one of the major railfan magazines, if I recall correctly. In that piece, he was relating the early piston failures of the engines when used extensively in long-haul service in the West, noting the comparatively high BMEP ratings and thus temperatures that the engines operated with in such service. The piston problems were apparently as much metallurgically driven as they were temperature driven, if those who are more engineering minded will allow that oversimplification, and were solved in time.
When you say "designed for shipboard use and not rail application" you are much closer to the mark. The nature of the construction of the engine, which, for example, made simple and quick inspection and replacement of pistons impossible when compared with the industry leaders, is commonly assumed to have been the locomotive program's undoing, which as Mr. Aldag has remarked bears some irony in the sense that it was solely the success (shipboard) of the engine itself that drove Fairbanks-Morse to develop a locomotive program centered around it in the first place.
(The Naval engines were offered in various numbers of cylinders, with further variation in power output per cylinder depending upon application and in many cases were actually producing less power per cylinder than the locomotive engines. The Naval engines also (especially in A-C generation) did not operate with rapidly and constantly changing speed and load. Thus, for the Naval engines, the regimen of teardown and inspection was often less frequent than it was for locomotive engines.)
Finally, there were many other factors that added to problems with F-M power, such as unfamiliarity to the shop workers (since the units were not common on most roads) and poor maintenance practices. In fact, and I've quoted from this before, I own a later F-M engine manual that has a list of "things not to do" or problems with actual maintenance practice which includes in its tone no small sense of bitterness. In this short section of this manual, it is perfectly obvious that F-M knew that railroad shop personnel were doing things in the field that led to often catastrophic failure of the engines (..."...the resetting of the shutdown point of a low oil pressure switch to a lower value, the increasing of the idle speed of an engine to keep the engine from shutting down because of low lube oil pressure will only bring disastrous results") and printed as much even though F-M knew that these things would continue. Even though these things were also probably being done to other makes of locomotive engine, those others being generally less expensive and difficult to maintain and more often available certainly helped F-M along the path to ending its locomotive production.