Dutch tolerance was in the past primarily motivated by a sense of social pragmatism IMHO. When it was profitable to drop the tolerance, the kind folk at the VoC were happy to do so. So you had people like Jan Pieterzoon encouraging Dutch traders (of lower social standing naturaly) to marry natives on the one hand, whilst advocating virtual genocide as a solution 'trade difficultues' on the other.
Quite a lot of Dutch words made it into Indonesian, words like administrasi, and rekening. Very...Dutch :p