You don't need two copies of the game. You can do local savefile transfer between two consoles (this is not the same thing as Cloud Saves, do not use Cloud Saves with edited savefiles.)
Also, if the custom firmware switch does not have anything bannable installed, it can safely go online in Sysnand CFW, so the second console is unnecessary if your reason for having a second untouched switch is so you have "one that can go online."