I agree, Borneo/Sarawak was never historically majority Muslim, pre-1900.
Cannot compare 2010 OTL stat in Borneo with pre-colonial Borneo. Too many PoDs happened OTL 20th century due to increase migrations by the Muslim Majority from Malaya or Java to Borneo.
I was wondering where you are going with Brooke's Kingdom. Borneo and Malaya are culturally different between locals pre-1900 with exceptions in coastal territories.
Wouldn't it be more practical ITTL to unify Borneo rather than go do an OTL Malaysia?
Since when did I say about unifying Borneo with Malaya?
But you did get the gist of it right; there were too many PODs between now and the modern day for conversion numbers to be like OTL.
As for whether or not it is practical to unify Borneo... well, you'll see.