I don't think I ever really thought about Two Worlds with that Sonic X detail in mind, but It still doesn't really make sense to me, but mostly because what X did doesn't make sense. Sonic and the landmass and people around Eggman's base are what managed to transfer over to "Earth" first, the second Chaos Control brought Mystic Ruins over, then they realized that if they let it stay like that time would freeze so they sent everyone back, and somehow that sent Mystic Ruins and Eggman's base back too? If there's anything from X that matches up, it's the vague "ability to go between the worlds" that Sonic supposedly has, because at the end of 51 or 52 or whatever he goes back on his own at Chris' vacation house and takes a month or something before he actually shows back up. that is to say it's no help in explaining how things work at all. Just another reminder of how little Sonic Team was actually willing to let go of anything for Sonic Boom, if the logic the show runners had to go off of was "Yeah it's exactly like the regular games but it's this specific setting for some reason but also don't bring anything up", I can only imagine what the Rise of Lyric writers had to go through. And they probably didn't even want Shadow!