Mostly because of what he accomplished by being victorious by military force. Napoleon Bonaparte emancipated the Jews because he brought freedom to all the continent, especially Germany. He was a Judeophile, and considered the Exodus story to be his personal inspiration to liberate oppressed Europeans from a brutal feudal system. He saw the American success at throwing off British colonial rule as the impetus to gather support for his military campaign to do the same in Europe. He also thought of himself as having a God-given destiny to emancipate the Jews and was well aware of their desire to rebuild the Temple in Jerusalem. You might call him the first evangelical Christian.

With every military victory, Napoleon preached his gospel of liberation to the poverty stricken masses he emancipated. Many of those freed by him joined his army to be a part of the movement, much like a cult leader operates. In Germany, at that time called “The Germanies”, Jews were especially oppressed, so Napoleon was welcomed as a messianic figure. Rabbis and Jewish leaders of the era called him an existential threat to Jewish culture, because Jews had always thrived under restrictions, and emancipation would drive a wedge between Jews, in particular the secular and religious. To this day the mainstream view of the orthodox is that Napoleon was a bad actor with regard to the Jewish people. As a condition of his army leaving Germany, he required a federated Germany and laws that gave Jews equal rights.

Jews of Germany, once emancipated, assimilated rapidly, entered academia, the arts, music, and politics. This was the golden age of ‘haskalah’, the Jewish enlightenment. By the mid 1840s the German aristocracy was in a state of panic, the Jews and commoners (to be fair, many Gentiles were also emancipated) were taking over the country which was now locked into a Parliamentary system. The response was a military right-wing crackdown on liberals. Many fled the country, which resulted in the German immigration wave in the US of the time. These liberals who were descended from Napoleon’s emancipated poor were now enamored of the USA and rhetoric against the slavery south, and the prospect of being a citizen of a fair and just nation lured them to come and fight for the Northern army.

You are right that this subject is rarely mentioned, as though there is a conspiracy of silence on this era of history. Probably a big reason is that it shows a militaristic nationalism long before the holocaust.