The heads of the Dutch East India company in Japan called on the Shōgun at Edo once a year. It was decreased to once every five years in the Bakumatsu, before being stopped altogether.

Engelbert Kaempfer, a German physician, accompanied the Dutch mission of 1691 and included an account in his book of Japan. The audience Kaempfer experienced was in two parts. First, the formal audience:

...they cry'd out Hollanda Captain [what the Japanese called the Dutch Ambassador], which was signal for him to draw near, and make his obeisances. Accordingly he crawl'd on his hands and knees, to a place shew'd him, between the presents rang'd in due order on one side, and the place, where the Emperor [Shōgun Tokugawa Tsunayoshi] sat, on the other, and then kneeling, he bow'd his forehead quite down to the ground, and so crawl'd backwards like a crab, without uttering one single word. So mean and short a thing is the audience we have of this mighty Monarch. Nor are there any more ceremonies observ'd in the audience he gives, even to the greatest and most powerful Princes of the Empire. For having been call'd into the hall, their names are cried out aloud, then they move on their hands and feet humbly and silently towards the Emperor's seat, and having shew'd their submission, by bowing their forehead down to the ground, they creep back again in the same submissive posture.

Kaempfer didn't seem to find the formal audience particularly bad. At the very least he recognized that all the other lords were received more or less the same way.

The one Kaempfer was really upset about was the second one that took place a few days after. He explains that formally only the formal audience was necessary, but the informal one had been happening for the last twenty years. To summarize (it's a bit long to type out) the group was lead into a room where the height of the tatami mats were arranged by the importance of the person sitting on it. The Europeans were told to sit on bare-wood floors, where the mats had been taken away. In other words, they were the lowest status of all present. In the audience were not only the shōgun and his counselors, but also his wives and ladies of the court (who sat behind screens) and sons, as well as pages and priests. Then there's the formal greetings as well as the usual ceremonies where the ambassador thanked the shōgun for allowing Dutch trade.

Afterwards, the Europeans were asked a bunch of very silly question (at least to Kaempfer), and ordered to

...stand upright, that he might have a full view of us; again to walk, to stand still, to compliment each other, to dance, to jump, to play the drunkard, to speak broken Japanese, to read Dutch, to paint, to sing, to put our cloaks on and off. Meanwhile we obey'd the Emperor's commands in the best manner we could, I join'd to my dance a love-song in High German. In this manner, with innumerable such other apish tricks, we must offer ourselves to contribute to the Emperor's and the Court's diversion.

Kaempfer was obviously very annoyed at being treated like a circus act/zoo. However, Kaempfer notes that:

The Ambassador, however, is free from these and the like commands, for as he represents the authority of his masters, some care is taken, that nothing should be done to injure or prejudice the same. Besides that he shew'd so much gravity in his countenance and whole behaviour, as was sufficient to convince the Japanese, that he was not at all a fit person to have such ridiculous and comical commands laid upon him.

Assuming other audiences took place in similar manners, that's what the buffoonery was. However it is important to note that Kaempfer did not believe the formal greetings of bowing and crawling were "buffoonery". The informal viewing zoo, "a perfect farce" in Kaempfer's words, were not required by the ambassador (though he was present). On other occasions Kaempfer also expresses what he thought were pointless actions but concluded that they were done purely because of how important the Japanese viewed social status. So, at least formally, the viewing zoo wasn't required for trade.

It looks like then Kaempfer's account was interpreted in an exaggerated way to vilify the Japanese to mark the end of WWII.

I am unable to identify the particular "act of buffoonery" to which this article refers, but I hope in this answer to contextualize the idea of an "act of buffoonery" as a meaningful gesture within the sociocultural system of Edo period Japan.

In Performing the Great Peace: Political Space and Open Secrets in Tokugawa Japan, Luke S. Roberts argues that Edo period (1603-1867) politics operated within two spheres. The first sphere, the omote, worked on the level of public performance. The second sphere uchi, operated on an internal or private level. Tokugawa authorities primarily cared about, and had jurisdiction over, omote actions.

Roberts offers several examples of the omote/uchi divide. A particularly useful example opens the introduction of his book. Roberts describes a local daimyō who was required by Tokugawa law to designate an heir before death. According to omote Tokugawa public records, the daimyō successfully named a successor before his death, and this was confirmed by a representative of the Shōgun. But the private uchi sources of the daimyō's clan indicate that the daimyō was long dead by the time the Shōgun's representative arrived to certify the selection of an heir. Which account of the daimyō's death is correct?, asks Roberts.

Roberts explains this discrepancy though the difference between omote and uchi realities. In the uchi world of the clan, the daimyō died on, say, the first of the month. But the clan performed a version of reality aimed at the Shōgun which argued that the daimyō was still alive until, say, the 15th. The clan's performance of deference toward Tokugawa authority was what mattered in this instance: the performance of a certain reality was more important to Tokugawa authorities than the accuracy of the performance. Thus, for a period of some two weeks, the daimyō could be privately dead but publicly alive.

I suspect that, in the instance which the Guardian describes, the Tokugawa or early Meiji government required a public display of Dutch obeisance to Japanese authority. Within Roberts's framework, it becomes clear that this performance of submission would have been a part of normal Japanese governing procedure rather than a premeditated plan to humiliate a European power. It is likely, in my opinion, that the Guardian reported a somewhat ordinary rite of Japanese governance as misinterpreted maliciousness.

Of course, if another historian has better insight on the particulars of the Dutch "act of buffoonery," this might clarify the meaning of the behavior. But, in the absence of more information, it is important to keep the structure of Tokugawa displays of state power in mind when interpreting these international actions.

Roberts, Luke S. Performing the Great Peace: Political Space and Open Secrets in Tokugawa Japan. Honolulu: University of Hawai'i Press: 2015.