Not really. They did that, but then people like missionary Zeno Żebrowski are considered heroes and influential figures. The Church alike is used more because it's such a classic fantasy evil guy, real Church did some corrupt things (but it also did a lot of good things), and Christianity in modern times is free real estate for mocking. Try that with Islam or Buddhism and there will be massive outrage. The cherry on cake is that Japanese do not take even their own history that seriously and there is plenty of remixes, "this historical guy, BUT genderbent/put literally anything else", parodies and what not in media, so they treat other cultures/regions/countries the same