Sometimes, this overlap was quite profound but not 100%. NeoGeo home consoles famously use the same hardware and software as their arcade counterparts, but the game cartridges were not pin-compatible. The Nintendo VS line were technically the same as a Famicom/NES, but not the same build; the software has subtle differences. Perhaps the Nintendo PlayChoice would count but again, it's not like they used NES mainboards to build those.
So, the idea of taking a Nintendo console mainboard and grafting it to SEGA-designed components so it can run in a dedicated arcade cabinet, is just wild to me.