Cascade of 3 MCP1663 to generate 100V @ 100 mA
The MCP1663 has a max working input voltage of 36 volts and, because this is the rating on the internal switching transistor this is also the maximum output voltage that could be produced so no, there is no benefit from cascading even two devices. 

Neither can you tee-off a second stage from the first stage by connecting the 2nd stage ground to the first stage output - how would the 2nd stage receive DC power to its input? No, this is a dead-end idea in my opinion.

Look for a step-up flyback converter - it will use a small transformer (well, actually a coupled inductor) to produce the 100 volts. Here's a flyback design that can produce 300 volts from 6 volts so maybe it can be adapted to produce 100 volts from a LiPo: -



But be prepared to have to use an output transistor in order to drive sufficient current into the primary. This will also be true of the next design.

There is also this circuit worthy of investigation/modification: -