Correct, the SD2SNES does replicate many expansion chips however those would already be expected exist on the cart bus connector. I was thinking of different scenario. For ease of example I will use the Genesis and CD addon.
Pretending for a moment the Analogue NT could replicate the Genesis hardware it would be doubtful that it could also do the Sega CD addon hardware. My thought was a cart connector addon that would add another FPGA to handle addition chips like those found in the Sega CD. This way hardware capabilities could be added to the Analogue NT Mini.
Again, I do not know the inner workings of FPGAs. It is possible that splitting hardware emulation accross multiple FPGAs would be very difficult, likely more so when working across the NES or Famicom cart connector. (Unless of bandwidth possibilities there)
I don't expect any of this is really cost effective, but it was more just entertaining to think about from a technical perspective.