How to get majority Christianity in China, Korea, Japan, and Southeast Asia during this time period and explain the effects. Would Christianity be more like a separate sect like Mormonism or a sect close to Christianity?
Well...the Korea situation can progress a la OTL, mostly. Simply keep the Japanese from annexing and brutalizing the peninsula. They repressed the Christian population, both there and in the Home Islands. [Rather ironically, Hiroshima and Nagasaki, iirc, had the largest Christian populations in Japan. The West actually nuked the cities that had the strongest (sort of) spiritual ties with them.] Also make Christianity more accepted? Imperialism that allows a European power to take much larger swaths of China, the Americans/Russians split or open up Korea earlier than OTL (with eventual reunification guaranteed, there was no Marxism when this was first proposed), and more missionaries in Japan. At least in East Asia, this can go a number of ways, especially speeding up certain OTL events. Following the US/Russia split of Korea, the idea of a Greek/Russian Orthodox North Korea is fucking hilarious. "We are the Best Korean Byzantium! All hail the Dear Basileus and Eternal Autokrator!" OTL ROK, especially in women above the age of 35, is already Christian up the wazoo.
Don't know much about SEAsia. Someone else may enlighten us. I'm genuinely curious to know about potential Christianization in areas apart from the Philippines. They're already devout Catholics, mostly.
Short of outright conquest and genocide at a level that would bankrupt the colonial powers, I don't think it's very possible to convert most of South East Asia to Christianity, especially Muslims. For the latter, you might want to go for a POD earlier than Raffles' ethnic policy (though I don't see a link to the DEA at all), even one that severely limits the early spread of Islam in Arabia, and maybe Buddhism.
Muslim hostility towards Christians in S.E.A. had been boiling over for centuries ever since the Portuguese arrived and seized Goa and Malacca from Muslim powers (Bijapur and Malacca sultanates). If the Portuguese focused more on gaining allies than actually seizing ports to control the trade routes, missionaries in the region might have more success against Muslims populations. Maybe converting the local Rajas and Sultans could work? Problem later on with the British and Dutch East India Companies is that they operate on the basis of business, and not interested in propagating Christianity. Doing the latter actually hurts their trading interests with the locals, not something they're keen at.
Mainland SEA is a whole other bag of 'nope'. Not sure about Myanmar and Indochina (I think there was actually some success in the latter), but Thailand/Siam is a very devout, Buddhist society, very hard for missionaries to penetrate as a whole.
Overall, very hard to repeat the example of the Philippines unless you're the Spanish, but even then, their resources are still pretty limited, and the Muslims in Mindanao are very resistant to conversion, nonetheless.