From a practicality standpoint I don't think swapping gems for bosses is a good idea. It's probably best just to ignore the boss room with the map plugin. However, a gem swapper plugin to replace leveling gems once you max out a gem's level I'm all for that. When I transfer items from my bot I always check the gems I have it leveling, and if they are close to 20 I spend more time than I want checking it so I can slip in another gem to level up. There may be a plugin that does this already I just havent got around to looking.