If the intention of SmartTrack is to reach the Airport Corporate Centre and in the future Square 1/Mississauga, then using the UPX routing is much better than Eglinton West.
SmartTrack in Mississauga is meant to hit the major office nodes that follow the 401. Basically Airport Corporate Centre to the Mississauga Road/401 area. The intention is to connect the region's major office areas from Mississauga to downtown Toronto to Markham. That's why they planned it to go along Eglinton West. Square 1 doesn't factor into this as they are not expecting much new office space there.