Boss

Would it be possible to make the Mystic Realm final boss (the one in Mystic Realm Zone) replace the normal Green Flower Zone boss and if so how would I do so?

Well I guess you could toss the mystic realm SOC into a wad and replace the eggmobile in GFZ3 with mapthing 209, but the whole boss battle was based around finding unique ways of approach to get around how Eggman was able to push you back, which is only the case when you're super and have no flashing time. Really, there's hardly any point.