I think it is all summed up by the
Global Statistics Booklet 2003-04.
If you download that PDF and then go to page 6 of 90 in that file you will see that in 2003-04, the last year available, the British Embassy in Tokyo granted 522 Settlement Visa applications and refused just 7.
In the main the Settlement Visa rejections are very different for so-called Visa Nationals, who need a visa to enter the UK for any reason whatsoever, and non-Visa Nationals who do not need a visa to enter for a number of reasons such as tourism.
That is, if a Japanese citizen wishes to get into the UK they can simply jump on a plane without a visa and invariably enter as a visitor. Japanese only need a visa for some specified reasons, including Settlement as a fiancé(e) or a spouse. That is there is far less likelihood of a non-Visa national entering into a "marriage of convenience" in order to gain entry into the UK. Indeed why would they bother? Accordingly the embassy would not be applying the same tests in Tokyo, as compared to say Bangkok, Thais being visa nationals, or in Moscow, Russians also being in that category.
In short, based upon the evidence you have mentioned, there is very little chance of your fiancée's application being rejected.