Sorry to be a PITA but to have this pipe going directly from the rocker cover into the inlet manifold is perhaps not that wise. These systems are called Positive Crankcase Ventilation (PCV) systems and are designed with special valves that prevent the vacuum from the manifold drawing oil from the rocker cover (similar to the vented loop in the raw water cooling system)
A diesel engine is not like a gasoline engine - it does not have a throttle plate in the manifold to control engine RPM. RPM is controlled by the volume of fuel that is injected. But if the engine starts to draw oil from the rocker cover into the inlet manifold, the engine will start enjoying the oil and will not need diesel to run on. Granted, manifold vacuum on a diesel is not as high as a gasoline engine but when the revs get up there the vacuum may be enough to draw oil from the rocker cover.
And if it does you may end up with a run-away engine. These can be character-building but are generally not recommended.
I am not a diesel specialist so the opinion above is offered reservedly. Just be sure you know what you're setting up. If the original system was a pipe hanging down the side of the engine, chances are it was never set up to be a PCV system.
You are right in some of what you are saying...
There is/was no PCV valve on this engine. The original setup was a small filter of a sponge type material which goes on the inside of the little cube piece sticking up from the head cover, or as it is called here valve cover, to prevent liquid oil from going up the hose and making a mess, that went up to the elbow and down the hose. The only oil that should be going anywhere in this situation should be in aerosol form, and it should not be much at all. A little smoke looking oil vapor, nothing solid or liquid at all. The vacuum is very low, and in the little one, two, and three cylinder engines it should not happen that it draws the oil up the tube. This is not a real positive crankcase ventilation system, where the vacuum is pulled intentionally to put a negative pressure in the system, in order to be positive you have ventilation. Yes I know having negatives to get positives can be confusing, but that is the way the world is, LOL.
However, since the Westerbeke/Universal representative has stated that running it into the manifold would be okay and that in any case it should definitely not be run through the filter, I said this would be the only good way to do it. Let me be clear in what I was saying, I personally would not run it there at all. Running it into the actual air filter, as it was in the one photo, would possibly pull a vacuum, like what you are talking about, and draw liquid oil up into the filter. I doubt it would pull enough to cause a runaway, on a naturally aspirated engine that would be tough to do in that manner unless there were underlying issues that allowed a lot more oil to go up than should. Theoretically, you could get a runaway out of the setup, and you really do not want one of those on your boat. They can be extremely destructive, dangerous, and more interesting than anything you really want to try, ever.
I would run it just like the manufacturer said to run it, things just work better when done like the pointy headed little pocket protector guys designed them to be done. Some people like to have the hose run over into the manifold to keep excess oil coming from the head cover from getting on stuff, but here is the problem with that, the oil is excess. That means it should not be coming out in that quantity, if you have a ton of blow by coming out that tube it means you have either worn valve guides and seals, worn valve seats, worn piston rings, or some other issue that is allowing compression to get into your crankcase and push more oil vapor out than ever should be coming out. Now if that is the case, guess what, this is one of the few things that would give your engine enough fuel to burn to keep running when you do not want it to run, and that is called a runaway. If you get a crankcase oil fed runaway it actually draws the oil off and burns it in the engine, but if the lubricating oil is getting burned....well that leaves the question of what is going to do the lubricating oil's job? The answer is NOTHING! You can toast the motor. Thankfully a full true runaway, where you have the engine cycling into ever higher RPM's almost never occurs in these little engines without turbos or superchargers on them. The type of runaway I am talking about always ends badly, and usually ends with the what was the internal parts ending up on the external part of the motor, pistons and rods flying out of the block. Like I said, these little motors just really do not get to that point very often, if ever, but they can be damaged by sucking their oil up the tube and into the motor.
If you have an excess of blow by coming out of that tube it needs to see a mechanic, not be routed into the intake. The issues that are beginning to appear when you first see those added little puffs of oil vapor coming out can be fixed if you get it done early. If you wait it can still be fixed, just bring me more money.