How to meaningfully compare Xilinx MCS files?
I would start by taking a look at the configuration documentation for those parts to get an idea about how the multiple bitstreams need to be stored in the flash to load all three FPGAs. It would also be a good idea to search for the bitstream header of the other two bitstreams in the combined file. That may actually be sufficient without requiring extra documentation. It might be easier to do this by converting the mcs files to bin files and then using a hex editor (unless you can find a hex editor that can edit the content of a hex file instead of the file itself). Once you know the offsets, then you can separate the bitstreams and then it's just a matter of doing a binary diff to see if they match. 

As far as comparing functionality, there is really no way to do that unless you can convert the bitstream back into a netlist. I don't think the Xilinx tools support this, so unless the bitstream format has been reverse-engineered, you're probably out of luck.