Bruh Batavia is Jakarta, Indonesia... As an Indonesian I'm glad that the name stuck :D
Unless you play The Smoke Room, 'Batavia' become confusing. In real life, Batavia is Jakarta in colonial era. Meanwhile, Batavia in The Smoke Room is equal to Netherlands (which Clifford's hometown). It seems, in this VN, Batavia is modern Netherlands.
Now, if The Echo Project makes another VNs with Batavia as setting, I'm not sure anymore which 'Batavia' that they referred.