Japan's a difficult spot; it was unknown to Europe at the time of the Treaty of Tacos, and while it did technically fall under the Portuguese sphere, both Spain and Portuguese Merchants competed for trade there (and, later, the Spanish Franciscans would quarrel with the predominantly-Portuguese Jesuits) - perhaps only legally possible given the Iberian Union. Japan being limited during the Sengoku Jidai is a bit of a misconception; it was only limited to the extent that the regional Daimyo turned away foreign missionaries; wherever the Jesuits were permitted, Portuguese merchants would usually follow. This was really only possible given the lack of authority that Kyoto had over the provinces; once the Tokugawa had unified Japan and crushed the remnants of the Western Army at Osaka in 1615, they were able to effectively impose their bans on Christianity, which ultimately culminated in the Shimabara Revolt in 1632 (which was then used as a convenient excuse to close the country).
The actual trade the Japanese engaged the Portuguese and Spanish in was by and large much more equitable than the Trade Companies in India, Indonesia and southern China, likely because they almost exclusively traded with the Daimyo that actually welcomed and protected them - the only things really resembling a foreign factory in Japan were William Adam's enterprise (granted, by that time he had settled down in Japan and been granted a title and a permit from the Shogunate, so it doesn't really count), and Dejima off the coast of Nagasaki where the Dutch resided - the latter only after the Tokugawa isolated Japan. There were, however, a number of Japanese enterprises and clans that, if allowed to have grown, would have likely turned into trading companies of their own or at least assumed the responsibilities of them; Red Seal Ships being the most prominent example (the Konishi and Date are both often cited as what-ifs in Japanese sources).
Nagasaki is a bit of an outlier in this period, given it was under Jesuit administration for a few years; administration of the small fishing port was given to the Jesuits by Suimtada Omura to ensure that the Catholics in Hizen - then being persecuted by Takanobu Ryuzoji - would have a safe haven. Sumitada retained the right to collect dues, but otherwise the Jesuits turned it into a heavily-fortified, cosmopolitan trading port that could compete with Hakata and Sakai practically overnight (owing in large part to the influx of Christian refugees, as Sumitada surrendered to Takanobu immediately after granting the Jesuits their port). However, it wasn't a foreign colony in any conventional sense; it was administered directly by the order locally, the native municipal council maintained authority, and the Jesuits later surrender the port to Hideyoshi Toyotomi without a fight (though the then-Superior Gaspar Coelho planned to resist the seizure of Nagasaki, but he was quickly reprimanded by the other missions and died naturally a few weeks before Valignano could return to Japan and strip him of his position). In this sense, Nagasaki better resembled the 'Free' merchant cities that sprung up across Japan during the Sengoku, like Sakai and Hakata, with the added caveat of a foreign, ecclesiocratic administration.
Originally the trade was primarily firearms on the Portuguese's part, but it quickly turned to saltpeter as the Japanese replicated and improved upon the firearms they had at an unprecedented rate, though they were always want for quality saltpeter. Other tradegoods included soap, glassworks, machinery (such as clocks), books, western armor, warhorses, and a number of Portuguese foods (apparently candies were particularly popular; Luis Frois even gained his first audience with Nobunaga Oda by presenting him with a flask of konpeito). On the Japanese's side, it was primarily lacquerware, swords, silk, Japanese silver, and occasionally tea paraphernalia and Japanese armor.
Dunno where you got the idea that the Portuguese Merchants didn't tell anyone else how to get to Japan: Spanish Franciscans and Florentine and Geonese Merchants all had notable presences there, it was an Englishman who more or less destroyed any prospects of a continued western presence in Japan, and the Dutch were the only westerners allowed to trade after Sakoku was imposed. That Francis Xavier first heard of Japan owing to an encounter with a Japanese exile in Malacca only four years after the Portuguese were moored on Tanegashima and the Jesuit Mission saw it's greatest reach under the leadership of the Neapolitan Alessandro Valignano (who organized a formal embassy to Europe from the Otomo Clan of Kyushu) should make it evident that it's location wasn't exactly a state secret (unlike, say, the recipe for Hot Chocolate).
But yeah; historically, there's no basis, but gameplay needs to come first.
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But yea I agree with you that one is a bit flawed
