Sounds a little abnormal to me, maybe valve train clatter? Maybe needs valve/tappet clearance adjusted? I think it's not so easy to get to them though. Intake runner seems to be the valve cover on this engine.
I wouldn't start adjusting valve clearances quite yet, because the noise can come from a variety of sources. Check and make sure there is nothing loose in the air cleaner assembly or another bracket, etc. on the top of the engine or ANYWHERE under the hood. Open the hood and carefully check things to make sure everything is tight and in its proper place. Diesel engine's vibrate and stuff gets loose. Often, that can be the cause of "rattle" sounds and noise. Start there.
Your engine would likely benefit from the use of a friction reducer additive. A good one is Prolong. I use it in everything I own and it helps to reduce wear and internal friction. Some don't believe in these products, to each their own. I have seen the examples first hand of reduced engine wear in my racing engines, especially in the valve train components, so I use it in all gas and diesel engines.
Just keep in mind this is an additive and you should NEVER overfill any engine oil, especially in diesel engines. So make sure to only add the proper amount when changing engine oil or if the oil level is low and new oil / lubricants / additives should be added. Follow the product directions.
Another issue can be the fuel quality. Diesel fuel nearly always benefits from increased cetane levels and specific additives which can improve fuel quality. Biodiesel contains as much as 10X the moisture in suspense (water) than dino diesel. This can cause increased "clatter" and "engine rattle" in the diesel engine combustion process. Pick a good fuel additive which you should ALWAYS use in ALL diesel fuel, year around. It can save you a lot of weather related issues with the fuel..............
There are several good diesel fuel additives, including the following;
Select one fuel additive which will meet the needs for your operating climate and stick with it. Avoid mixing and blending fuel additives as they work in different ways. Those which are emulsifiers bind the water in the fuel to the fuel and force it through the filters to be burned in the combustion process. Personally, I won't use any emulsifier products in my diesel engines as water is extremely abrasive in high pressure fuel systems. It wears out injectors, injection pumps and can even wear pistons and cylinder walls.
The easiest way to identify an emulsifier product is it uses alcohol family products as one or more of its primary ingredients. If the ingredients list items which end in an "ol" its very likely an alcohol based product and in the emulsifier category. For example, one of the most famous emulsifiers is "Heet", the winter time gasoline additive to prevent winter fuel issues. The specific active ingredients of HEET and ISO-HEET are methanol and isopropanol, respectively. Note the "ol's?"
The diesel fuel supplements I listed above are NOT emulsifier products. They work by separating the water / moisture from the fuel so it can be drained from the fuel tank or out of the fuel separator, where the engine fuel filter is held.
Bottom line, most diesel engine "rattles" are normal and part of their operation. However, it is wise to use fuel additives which improve fuel quality and consider reducing engine friction with a good motor oil, designed for the application as well as considering high quality lubrication additives to help reduce wear. Just make sure to start with the basics and make sure nothing is loose or broken under the hood, adding to the noise you hear..............
It is extremely hard to tell anything from a cell phone recording, especially when it is only 16 seconds from that tiny microphone held beside the steering wheel. 3 cylinder Yanmar diesel engines are notorious for their rattling and clattering.
It might be a little more clattery then mine, but simple fuel quality can cause that.
I would put some Cetane boost in it and see if that doesn't clear it up.
I have used this stuff off and on or as needed for 20 years always quieten downs the clatter.
Difficult to diagnose with a video. Does it quiet down when it's warmed up to normal operating temperature? Try one of these methods to narrow it down. Could be a rattle as diesels tend to be a bit shaky. Let us know what you find out.