"I also wonder, that if you can test oil for proper additives, if you can also have field tests for fuel in oil. "
Yes, but it takes a bit of practice and is not particularly accurate. Here is a link to an explanation of how to do it.
http://www.worldlube.com/self-test.html "Is added filtration going to filter out the blowby byproducts such as fuel?"
No, nothing aside from distillation will remove fuel from the oil. If you have fuel dilution, change the oil.
"If the tests show some additive levels to be low, can some be added?"
On larger engines like the slow speed or medium speed engines used on larger ships, a partial oil change is done to restore the TBN to within limits. It is not worth bothering with for the smaller engines used on yachts. Just change the oil according to the engine manufacturers reccommendation.
"Are some oils, such as synthetic oils preferable in cases such as this?"
Synthetic oils are excellent for high temperature applications. They may not be economical for "normal" propulsion applications unless you are running E ratings for extended periods at high temperature and then this is the wrong thread for that discussion.
"My CAT guy thinks that having pyrometers installed will help determine the best rpm's at which engines are operating well and burning the fuel efficiently, so as to prevent glazing and fuel blowby."
Pyrometers measure exhaust gas temperature at the exhaust valve. Low loads equate to lower exhaust temperatures than high loads. Pyrometers provide useful information for determining overload conditions or poor performance on a cylinder and for balancing cylinders but are not very useful for tweaking low power settings.
What he might be talking about is the condition where at lower loads the exhaust gas temperature might be very slightly higher than it would be at a slightly higher load. This is due to the fact that turbocharged engines use a technique called valve overlap to provide better scavenging. The exhaust and inlet valves are open at the same time for a period and this allows complete removal of exhaust gases and the cooler scavenging air blows over the exhaust valves and cools them and the pyrometer sensor. At low power there isn't as much scavenging air pressure developed by the turbo so the exhaust may actually be a few degrees higher. It's hard to see on an analog guage though.
"I also wonder why some charter boats go 10k hours between overhauls with big engines and tons of trolling."
Because this isn't really much of an issue except on a few boating bulletin boards. That and the fact that unlike generators which operate at constant speeds regardless of loads, propulsion engines operate at varying loads and speeds which is a very good way to avoid the problems generator engines suffer from when operated at very low loads for most of their lives.