1. According to Wikipedia, the spread of Islam in Indonesia were attributed to Arab traders. The main spread of the religion were between the years of 1200–1600. In scenario 1., it does not make much sense for Indonesia to be Islamic, as the Arabs that would have traded with them would have been Jewish or at least not have held as much influence as they did.
Potential outcome: Indonesia would either be Jewish or have stayed as their folk religion (Hindu/Buddhist/Animist).
I think it should be a simple boolean of is Islam successful? If Yes Indonesia is Muslim, If No it is its native religion of Pagan/Dharmic.
Why? Two reasons.
Aside from Christianity, no other religion that succeeds in the peninsula is particularly prosyltising. Judaism, Zoroastrianism, the rare Gnostics like the Manicheans, rare "others" like the Yazidi and Druze are all either "you're born into it" religions or just not historically easily spread.
Islam has the concept of the Ummah and Christianity of Evangelism. They're your only two real spreaders.
However, (second reason) a Christian Arabia would almost certainly be one that has a different culture than the native Arabs, and would likely replace them. This would have unpredictable results on the Indonesian trade situation. It's possible that in this time period that Western Christianity could not make it to Indonesia.
Nestorians are a different matter I guess, but it'd be such a rare case that they'd become dominant, should it really get our attention?
Now, if you wanted to make things real complex you could do a "which is dominant?" clause for Sunni, Shia, Ibadi, Zikri, Hurufi or Nestorian in the Arabian Peninsula and make that the religion of Indonesia. If none are dominant, you default to Dharmic/Pagan.
2. If India were under the complete control of Islamic sultanates, it might have made sense for them to continue spreading their religion eastward. Imagine if an Islamic religion would in this case have pushed as far east as Indochina, or even into southern china? This could also be based on the relative strength of Islam in general.
Potential outcome: More Indochinese nations have Islam as their state religion, with a provincial religious setup not unlike that of 1444 vanilla India. Several Islamic provinces in China.
Sorry, China's just too static and centralised. It doesn't convert unless it wants to. I say we leave China alone.
3. The Chinese dynasties at one time promoted Manichaeism among their people. But as the power of Manichaen nations fell, the practice was abandoned and even persecuted. If there's a strong Manichean presence on the map, parts of China might be Manichean? If the Manichean presence is very strong, China might potentially turn Manichean?
Potential outcome: A heavier Manichean presence in the east.
Leave China alone! Leave it alone!