If I may recap...
1. It sounds like Star Tours will be rethemed/demolished at some point in time after SWL opens.
2. Muppets Courtyard is staying put.
Thematically, having Muppets separate Star Tours from the rest of SWL would be a concrete no in my mind. Then again, from what I've read here it seems logical to keep the Muppets in operation, open SWL, and then decide what to do with Star Tours. Hell, maybe at that point Indy 5 will be in theaters and Bob can decide if an Indy style dark ride could takeover Star Tours.
I also am confused regarding the second entrance/exit into SWL. We know that one of the entrances will be a corridor using the previous SoA. Is the other entrance supposed to connect to the far side of TSL? Lastly, what becomes of the path through Pixar Place? Will this be rerouted once Toy Story opens to make way for additional expansion?