After reading the manual page here is what I think. However note I'm not a mechanic so just amateur thoughts.
They say NOT to shut down after a long/high speed run (i.e. no cool down).
What I have read here before, which makes sense to me, is that most of us will have run up to speed at some point during the day, but then do run at a reasonable length of time at low speed with almost no load (coming in to the marina or anchorage, maneuvering, etc.). That seems like it would take care of the "don't shut down immediately after high speed."
So that leaves the brief "race" before cool down and shutting off, which is your original question. They say it's to remove carbon deposits. So, if you had made a high speed run earlier, are there any to remove? Is this only for people who have trolled all day with no speed run?
It sounds analogous to that quick "rev" that people of my parents' generation always did to their cars before shutting them off. You know, put it in Park, hit the accelerator and a quick "vrooom!" and then shut it off. Those were gas engines, but was there some basis for it?
I guess at the end of this post, I have the same question as you. Is there a benefit to these quick "vrooms"? Do they need to be done if you had already run at high speed during that day (but then idled into the marina or anchorage). Is it a good idea, a neutral one, or a bad one?
(I don't see this as them recommending a long period of high RPM's. I interpret it as quick bursts a la the parents and the car.)
If it were my engine I would (in addition to posting here, which is a good idea) contact Yanmar and see if they can flesh it out a bit. Does it need to be done if you have already run at high speed? What are the downsides? Etc. I'd probably also call a trusted Yanmar mechanic to get their take. Wording my questions so as not to "lead" one way or another.