Unless I am overlooking something really obvious, I don't think that there is anything special about the DIP switches; they simply act to pull one address pin low (or high).
When you burn an image to an EPROM, the burner sees the address pins in reverse lexicographic order (A15, A14, A13, ... , A3, A2, A1, A0) and the least-significant address bits vary most quickly. So the first byte in the file is at address 0b000000000000000, the next is at 0b000000000000001, and so on.
But there is no particular reason that your application needs to use the pins in the same way. You could use them in the order (A8, A7, A6, A15, A14, A13, A12, A11, A10, A9, A5, A4, A3, A2, A1, A0) if that made the circuit simpler to lay out. Or in the reverse order, or any permutation. At that point, you have two choices for how to burn the image. The first and most intuitive is to plug your adapter, with DIP switches, into the EPROM burner and burn your banks as separate 2732 images (changing the DIPs appropriately). Now you are guaranteed to burn the image in the same way that the application will see it.
The second way is to pre-swizzle the ROM file to send each byte to its "image" in the new chip. The way you would do this is to write a program that takes in a ROM file and loops over each byte, with a counter going up from 0; each byte then gets written out to the target ROM file at a position that you calculate by swapping the address bit of the application with the address bit of the ROM.